Small modification for GCG ASCII (libtype=5) header line.
October 6, 2006 CVS fa34t26b3
New Windows programs available using Intel C++ compiler. First
threaded programs for Windows; first SSE2 acceleration of SSEARCH for
Windows.
July 18, 2006 CVS fa34t26b2
More powerful environment variable substitutions for FASTLIBS files.
The library file name parsing programs now provide the option for
environment variable substitions. For example, SLIB2=/slib2 as an
environment variable (e.g. export SLIB2=/slib2 for ksh and bash), then
fasta34 -q query.aa '${SLIB2}/swissprot.fa' expands as expected.
While this is not important for command lines, where the Unix shell
would expand things anyway, it is very helpful for various
configuration files, such as files of file names, where:
<${SLIB2}/blast
swissprot.fa
now expands properly, and in FASTLIBS files the line:
expands properly. Currently, Environment variable expansion only
takes place for library file names, and the <directory in a file of
file names.
July 2, 2006 fa34t26b0
This release provides an extremely efficient SSE2 implementation of
the Smith-Waterman algorithm for the SSE2 vector instructions written
by Michael Farrar (farrar.michael@gmail.com). The SSE code speeds up
Smith-Waterman 8 - 10-fold in my tests, making it comparable to Eric
Lindahl's Altivec code for the Apple/IBM G4/G5 architecture.
May 24, 2006 fa34t25d8
In addition, support for ASN.1 PSSM:2 files provided by the NCBI
PSI-BLAST WWW site is included. This code will not work with
iteration 0 PSSM's (which have no PSSM information). For ASN.1
PSSM's, which provide the matrix name (and in some cases the gap
penalties), the scoring matrix and gap penalties are set appropriately
if they were not specified on the command line. ASN.1 PSSM's are type 2:
ssearch34 -P "pssm.asn1 2" .....
May 18, 2006
Support for NCBI Blast formatdb databases has been expanded. The
FASTA programs can now read some NCBI *.pal and *.nal files, which are
used to specify subsets of databases. Specifically, the
swissprot.00.pal and pdbaa.00.pal files are supported. FASTA supports
files that refer to *.msk files (i.e. swissprot.00.pal refers to
swissprot.00.msk); it does not currently support .pal files that
simply list other .pal or database files (e.g. FASTA does not support
nr.pal or swissprot.pal).
Nov 20, 2005
Changes to support asymmetric matrices - a scoring matrix read in from
a file can be asymmetric. Default matrices are all symmetric.
Sept 2, 2005
The prss34 program has been modified to use the same display routines
as the other search programs. To be more consistent with the other
programs, the old "-w shuffle-window-size" is now "-v window-size".
prss34/prfx34 will also show the optimal alignment for which the
significance is calculated by using the "-A" option.
Since the new program reports results exactly like other
fasta/ssearch/fastxy34 programs, parsing for statistical significance
is considerably different. The old format program can be make using
"make prss34o".
May 5, 2005 CVS fa34t25d1
Modification to the -x option, so that both an "X:X" match score and
an "X:not-X" mismatch score can be specified. (This score is also used
to give a positive score to a "*:*" match - the end of a reading frame,
while giving a negative score to "*:not-*".
Jan 24, 2005
Include a new program, "print_pssm", which reads a blastpgp binary
checkpoint file and writes out the frequency values as text. These
values can be used with a new option with ssearch34(_t) and prss34,
which provides the ability to read a text PSSM file. To specify a
text PSSM, use the option -P "query.ckpt 1" where the "1" indicates a
text, rather than a binary checkpoint file. "initfa.c" has also been
modified to work with PSSM files with zero's in the in the frequency
table. Presumably these positions (at the ends) do not provide
information. (Jan 26, 2005) blastpgp actually uses BLOSUM62 values
when zero frequencies are provided, so read_pssm() has been modified
to use scoring matrix values for zero frequencies as well.
Nov 4-8, 2004
Incorporation of Erik Lindahl "anti-diagonal" Altivec code for
Smith-Waterman, only. Altivec SSEARCH is now faster than FASTA for
Aug 25,26, 2004 CVS fa34t24b3
Small change in output format for p34comp* programs in
">>>query_file#1 string" line before alignments. This line is not present
in the non-parallel versions - it would be better for them to be consistent.
Dec 10, 2003 CVS fa34t23b3
Cause default ktup to drop for short query sequences. For protein queries < 50, ktup=1;
for DNA queries < 20, 50, 100 ktup = 1, 2, 3, respectively.
Dec 7, 2003
A new option, "-U" is available for RNA sequence comparison. "-U"
functions like "-n", indicating that the query is an RNA sequence. In
addition, to account for "G:U" base pairs, "-U" modifies the scoring
matrices so that a "G:A" match has the same score as a "G:G" match,
and "T:C" match has the same score as a "T:T" match.
Nov 2, 2003
Support for more sophisticated display options. Previously, one could
have only on "-m #" option, even though several of the options were
orthogonal (-m 9c is independent of -m 1 and -m2, which is independent
of -m 6 (HTML)). In particular -m 9c can be combined with -m 6, which
can be very helpful for runs that need HTML output but can also
exploit the encoding provided by -m 9c.
The "-m 9" option now also allows "-m 9i", which shows the standard
best score information, plus percent identity and alignment length.
Sept 25, 2003
A new option is available for annotating alignments. -V '@#?!'
can be used to annotate sites in a sequence, e.g:
This annotation is mostly designed to display post-translational
modifications detected by MassSpec with FASTS, but is also available
with FASTA and SSEARCH.
June 16, 2003 version: fasta34t22
ssearch34 now supports PSI-BLAST PSSM/profiles. Currently, it only
supports the "checkpoint" file produced by blastall, and only on
certain architectures where byte-reordering is unnecessary. It has not
been tested extensively with the -S option.
Will use the frequency information in the blast.chkpt file to do a
position specific scoring matrix (PSSM) search using the
Smith-Waterman algorithm. Because ssearch34 calculates scores for
each of the sequences in the database, we anticipate that PSSM
ssearch34 statistics will be more reliable than PSI-Blast statistics.
The Blast checkpoint file is mostly double precision frequency
numbers, which are represented in a machine specific way. Thus, you
must generate the checkpoint file on the same machine that you run
ssearch34 or prss34 -P query.ckpt. To generate a checkpoint file,
run:
(This searches swissprot for 2 iterations ("-j 2" using a E()
threshold 1e-6 saving the resulting position specific frequencies in
query.ckpt. Note that the original query.fa and query.ckpt must
match.)
Apr 11, 2003 CVS fa34t21b3
Fixes for "-E" and "-F" with ssearch34, which was inadvertantly disabled.
A new option, "-t t", is available to specify that all the protein
sequences have implicit termination codons "*" at the end. Thus, all
protein sequences are one residue longer, and full length matches are
extended one extra residue and get a higher score. For
fastx34/tfastx34, this helps extend alignments to the very end in
cases where there may be a mismatch at the C-terminal residues.
-m 9c has also been modified to indicate locations of termination
codons ( *1).
Mar 17, 2003 CVS fa34t21b2
A new option on scoring matrices "-MS" (e.g. "BL50-MS") can be used to
turn the I/L, K/Q identities on or off. Thus, to make "fastm34" use
the isobaric identities, use "-s M20-MS". To turn them off for "fasts34",
use "-s M20".
Jan 25, 2003
Add option "-J start:stop" to pv34comp*/mp34comp*. "-J x" used to
allow one to start at query sequence "x"; now both start and stop can
be specified.
Nov 14-22, 2002 CVS fa34t20b6
Include compile-time define (-DPGM_DOC) that causes all the fasta
programs to provide the same command line echo that is provided by the
PVM and MPI parallel programs. Thus, if you run the program:
fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12
the first lines of output from FASTA will be:
# fasta34_t -q gtt1_drome.aa /slib/swissprot
FASTA searches a protein or DNA sequence data bank
version 3.4t20 Nov 10, 2002
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
This has been turned on by default in most FASTA Makefiles.
Aug 27, 2002
Modifications to mshowbest.c and drop*.c (and p2_workcomp.c,
compacc.c, doinit.c, etc.) to provide more information about the
alignment with the -m 9 option. There is now a "-m 9c" option, which
displays an encoded alignment after the -m 9 alignment information.
The encoding is a string of the form: "=#mat+#ins=#mat-#del=#mat".
Thus, an alignment over 218 amino acids with no gaps (not necessarily
100% identical) would be =218. The alignment:
would be encoded: "=23+9=13-2=10-1=3+1=5". The alignment encoding is
with respect to the beginning of the alignment, not the beginning of
either sequence. The beginning of the alignment in either sequence is
given by the an0/an1 values. This capability is particularly useful
for [t]fast[xy], where it can be used to indicate frameshift positions
"/#\#" compactly. If "-m 9c" is used, the "The best scores" title
line includes "aln_code".
Aug 14, 2002 CVS tag fa34t20
Changes to nmgetlib.c to allow multiple query searches coming from
STDIN, either through pipes or input redirection. Thus, the command
produces 11 searches. If you use the multiple query functions, the
query subset applies only to the first sequence.
Unfortunately, it is not possible to search against a STDIN library,
because the FASTA programs do not keep the entire library in memory
and need to be able to re-read high-scoring library sequences. Since
it is not possible to fseek() against STDIN, searching against a STDIN
library is not possible.
Aug 5, 2002
fasts34(_t) and fastm34(_t) have been modified to allow searches with
DNA sequences. This gives a new capability to search for DNA motifs,
or to search for ordered or unordered DNA sequences spaced at
arbitrary distances.
June 25, 2002
Modify the statistical estimation strategy to sample all the sequences
in the database, not just the first 60,000. The histogram is still
based only on the first 60,000 scores and lengths, though all scores
an lengths are shown. The fit to the data may be better than the
histogram indicates, but it should not be worse.
June 19, 2002
Added "-C #" option, where 6 <= # <= MAX_UID (20), to specify the
length of the sequence name display on the alignment labels. Until
now, only 6 characters were ever displayed. Now, up to MAX_UID
characters are available.
Mar 16, 2002
Added create_seq_demo.sql, nt_to_sql.pl to show how to build an SQL
protein sequence database that can be used with with the mySQL
versions of the fasta34 programs. Once the mySQL seq_demo database
has been installed, it can be searched using the command:
fasta34 -q mgstm1.aa "seq_demo.sql 16"
mysql_lib.c has been modified to remove the restriction that mySQL
protein sequence unique identifiers be integers. This allows the
program to be used with the PIRPSD database. The RANLIB() function
call has been changed to include "libstr", to support SQL text keys.
Due to the size of libstr[], unique ID's must be < MAX_UID (20)
characters.
A "pirpsd.sql" file is available for searching the mySQL distribution
of the PIRPSD database. PIRPSD is available from
ftp://nbrfa.georgetown.edu/pir_databases/psd/mysql.
Summary - Major Changes in FASTA version 35 (August, 2007)
Accurate shuffle based statistics for searches of small libraries (or pairwise comparisons).
Inclusion of lalign35 (SIM) into FASTA3. Accurate statistics for
lalign35 alignments. plalign has been replaced by
lalign35 and lav2ps.
Two new global alignment programs: ggsearch35 and glsearch35.
February 7, 2008
Allow annotations in library, as well as
query sequences. Currently, annotations are only available within
sequences (i.e., they are not read from the feature table), but they
should be available in FASTA format, or any of the other ascii text
formats (EMBL/Swissprot, Genbank, PIR/GCG). If annotations are
present in a library and the annotation characters includes '*', then
the -V '*' option MUST be used. However, special characters other
than '*' are ignored, so annotations of '@', '%', or '@' should be
transparent.
In translated sequence comparisons, annotations are only available for
the protein sequence.
January 25, 2007
Support protein queries and sequence
libraries that contain 'O' (pyrrolysine) and 'U' (selenocysteine).
('J' was supported already). Currently, 'O' is mapped automatically to
'K' and 'U' to 'C'.
Dec. 13, 2007 CVS fa35_03_02m
Add ability to search a subset of a library using a file name and a
list of accession/gi numbers. This version introduces a new filetype,
10, which consists of a first line with a target filename, format, and
accession number format-type, and optionally the accession number
format in the database, followed by a list of accession numbers. For
example:
Tells the program that the target database is swissprot.lseg, which is
in FASTA (library type 0) format.
The accession format comes after the ":". Currently, there are four
accession formats, two that require ordered accessions (:1, :2), and
two that hash the accessions (:3, :4) so they do not need to be
ordered. The number and character after the accession format
(e.g. "4|") indicate the offset of the beginning of the accession and
the character that terminates the accession. Thus, in the typical
NCBI Fasta definition line:
The offset is 4 and the termination character is '|'. For databases
distributed in FASTA format from the European Bioinformatics
Institute, the offset depends on the name of the database, e.g.
Accession formats 1 and 3 expect strings; accession formats 2 and 4
work with integers (e.g. gi numbers).
December 10, 2007
Provide encoded annotation information with
-m 9c alignment summaries. The encoded alignment information makes it
much simpler to highlight changes in critical residues.
August 22, 2007
A new program is
available, lav2svg, which creates SVG (Scalable Vector
Graphics) output. In addition, ps_lav,
which was introduced May 30, 2007, has been replaced
by lav2ps. SVG files are more easily edited with Adobe
Illustrator than postscript (lav2ps) files.
July 25, 2007 CVS fa35_02_02
Change default gap penalties for OPTIMA5 matrix to -20/-2 from -24/-4.
July 23, 2007
Add code to support to support sub-sequence ranges for "library"
sequences - necessary for fully functional prss (ssearch35) and
lalign35. For all programs, it is now possible to specify a subset of
both the query and the library, e.g.
lalign35 -q mchu.aa:1-74 mchu.aa:75-148
Note, however, that the subset range applied to the library will be
applied to every sequence in the library - not just the first - and
that the same subset range is applied to each sequence. This probably
makes sense only if the library contains a single sequence (this is
also true for the query sequence file).
July 3, 2007 CVS fa35_02_01
Merge of previous fasta34 with development version fasta35.
June 26, 2007
Add amino-acid 'J' for 'I' or 'L'.
Add Mueller and Vingron (2000) J. Comp. Biol. 7:761-776 VT160 matrix,
"-s VT160", and OPTIMA_5 (Kann et al. (2000) Proteins 41:498-503).
June 7, 2007
ggssearch35(_t), glsearch35(_t) can now use PSSMs.
May 30, 2007 CVS fa35_01_04
Addition of ps_lav
(now lav2ps or lav2svg) -- which can be used to plot the lav
output of
lalign35 -m 11.
lalign35 -m 11 | lav2ps
replaces plalign
(from FASTA2).
May 2, 2007
The labels on the alignment scores are much more informative (and more
diverse). In the past, alignment scores looked like:
where the highlighted text was either: "Smith-Waterman" or "banded
Smith-Waterman". In fact, scores were calculated in other ways,
including global/local for fasts and fastf. With the addition of
ggsearch35,glsearch35, and lalign35, there are many more ways to
calculate alignments: "Smith-Waterman" (ssearch and protein fasta),
"banded Smith-Waterman" (DNA fasta), "Waterman-Eggert",
"trans. Smith-Waterman", "global/local", "trans. global/local",
"global/global (N-W)". The last option is a global global alignment,
but with the affine gap penalties used in the Smith-Waterman
algorithm.
April 19, 2007 CVS fa34t27br_lal_3
Two new programs, ggsearch35(_t) and glsearch35(_t) are now available.
ggsearch35(_t) calculates an alignment score that is global in the
query and global in the library; glsearch35(_t) calculates an alignment
that is global in the query and local, while local in the library
sequence. The latter program is designed for global alignments to domains.
Both programs assume that scores are normally distributed. This
appears to be an excellent approximation for ggsearch35 scores, but
the distribution is somewhat skewed for global/local (glsearch)
scores. ggsearch35(_t) only compares the query to library sequences
that are beween 80% and 125% of the length of the query; glsearch
limits comparisons to library sequences that are longer than 80% of
the query. Initial results suggest that there is relatively little
length dependence of scores over this range (scores go down
dramatically outside these ranges).
March 29, 2007 CVS fa34t27br_lal_1
At last, the lalign (SIM) algorithm has been moved from FASTA21 to
FASTA35. A plalign
equivalent is also available using lalign -m 11 | lav2ps
or | lav2svg.
The statistical estimates for lalign35 should be much more accurate
than those from the earlier lalign, because lambda and K are estimated
from shuffles.
In addition, all programs can now generate accurate statistical
estimates with shuffles if the library has fewer than 500 sequences.
If the library contains more than 500 sequences and the sequences are
related, then the -z 11 option should be used.
pFASTA v34 Change Log
Latest Updates - FASTA version 36.3.8h (March, 2019)
The FASTA programs have been released under the Apache2.0 Open
Source License. The COPYRIGHT file, and copyright notices in
program files, have been updated to reflect this change.
fasta-36.3.8h includes bug fixes for translated alignments
with termination codons, the ability to use scripts as query
and library sequences, and new scripts for extracting genomic
DNA sequences given chromosome coordinates.
fasta-36.3.8g includes bug fixes for sub-alignment scoring and
psisearch2 scripts, new annotation scripts for exons, and
fixes enabling very low statistical thresholds with ggsearch36
and glsearch36.
fasta-36.3.8e/scripts includes updated scripts for
capturing domain and feature annotations using the
EBI/proteins API (https://www.ebi.ac.uk/proteins/api/) to get
Uniprot annotations and exon locations.
The fasta-36.3.8e/psisearch2/ directory now
provides psisearch2_msa.pl
and psisearch2_msa.py, functionally identical scripts
for iterative searching with psiblast
or ssearch36. psisearch2-msa.pl offers an
option, --query_seed, that can dramatically reduce
false-positives caused by alignment overextension, with very
little loss of search sensitivity.
The fasta-36.3.8d/scripts/ directory now provides a
script, annot_blast_btop2.pl that allows annotations and
sub-alignment scoring on BLAST alignments that use the tabular format
with BTOP alignment encoding.
Alignment sub-scoring scripts have been extended to allow
overlapping domains. This requires a modified annotation file format.
The "classic" format placed the beginning and end of a domain on different lines:
1 [ - GST_N
88 ] -
90 [ - GST_C
208 ] -
Since the closing "]" was associated with the previous "[", domains could not overlap.
The new format is:
1 - 88 GST_N
90 - 208 GST_C
which allows annotations of the form:
1 - 88 GST_N
75 - 123 GST-middle
90 - 208 GST_C
New annotation scripts are available in
the fasta-36.3.8/scripts directory,
e.g. ann_pfam_www_e.pl (Pfam) and ann_up_www2_e.pl
(Uniprot) to support this new format. If the domain annotations
provided by Pfam or Uniprot overlap, then overlapping domains are
provided. The _e.pl new scripts can be directed to provide
non-overlapping domains, using the boundary averaging strategy in
the older scripts, by specifying the --no-over option.
Updates - FASTA version 36.3.6f (August, 2014)
FASTA version 36.3.6f extends previous versions in several ways:
There is a new command line option, -XI, that causes the
alignment programs to report 100% identity only when there are no
mismatches. In previous versions, one mismatch in 10,000 would round
up to 100.0% identity; with -XI, the identity will be
reported as 99.9%.
The option to provide alignment encodings (-m 9c, or -m 9C forCIGAR
strings) has been extended to provide mis-match information in the
alignment encoding using the -m 9d (classic FASTA alignment encoding)
or -m 9D (CIGAR string). For protein alignments, which are often <
40% identity, enabling mismatch encoding produces very long CIGAR
strings.
Provide more scripts for annotating proteins using either UniProt or
Pfam web resources.
Additional bug fixes are documented in fasta-36.3.6f/doc/readme.v36
Updates - FASTA version 36.3.6 (July, 2013)
FASTA version 36.3.6 provides two new features:
A new script-based strategy for including annotation information.
Domain annotation information can be used to produce partition the
alignment, and partition the scores of the alignment (sub-alignment
scores). Sub-alignment scores can be used to identify regions of
alignment over-extension, where a homologous domain aligns, but the
alignment extends beyond the homologous region into an adjacent
non-homologous domain.
Several scripts are provided (e.g. scripts/ann_feats_up_www.pl) that
can be used to add Uniprot feature and domain annotations to searches
of SwissProt and Uniprot.
(fasta-36.3.5 January 2013)
The NCBI's transition from BLAST to BLAST+ several years ago broke the
ability of ssearch36 to use PSSMs, because psiblast
did not produce the binary ASN.1 PSSMs that ssearch36 could
parse. With the January 2013 fasta-36.3.5f,
release ssearch36 can read binary ASN.1 PSSM files produced
by the NCBI datatool utility.
See fasta_guide.pdf for more information
(look for the -P option).
Summary - Major Changes in FASTA version 36.3.5 (May, 2011)
By default, the FASTA36 programs are no longer interactive. Typing
fasta36 presents a short help message, and
fasta36 -help presents a complete list of options. To see the interactive prompts, use
fasta36 -I.
Likewise, the score histogram is no longer shown by default; use
the -H option to show the histogram (or compile with
-DSHOW_HIST for previous behavior).
The _t (fasta36_t) versions of the programs are
built automatically on Linux/MacOSX machines and
named fasta36, etc. (the programs are threaded by default,
and only one program version is built).
Documentation has been significantly revised and updated.
See doc/fasta_guide.pdf for a description of the programs and options.
Display of all significant alignments between query and library
sequence. BLAST has always displayed multiple high-scoring
alignments (HSPs) between the query and library sequence; previous
versions of the FASTA programs displayed only the best alignment,
even when other high-scoring alignments were present. This is the
major change in FASTA36. For most programs
(fasta36, ssearch36,
[t]fast[xy]36), if the library sequence contains additional
significant alignments, they will be displayed with the alignment
output, and as part of -m 9 output (the initial list of high
scores).
By default, the statistical threshold for alternate alignments
(HSPs) is the E()-threshold / 10.0. For proteins, the default
expect threshold is E()< 10.0, the secondary threshold for showing
alternate alignments is thus E() < 1.0. Fror translated
comparisons, the E()-thresholds are 5.0/0.5; for DNA:DNA 2.0/0.2.
Both the primary and secondary E()-thresholds are set with the
-E "prim sec" command line option. If the secondary
value is betwee zero and 1.0, it is taken as the actual
threshold. If it is > 1.0, it is taken as a divisor for the primary
threshold. If it is negative, alternative alignments are disabled
and only the best alignment is shown.
New statistical options, -z 21, 22, 26, provide a second E()-value
estimate based on shuffles of the highest scoring sequences.
New output options. -m 8 provides the same output format as
tabular BLAST; -m 8C mimics tabular blast with comment
lines. -m 9C provides CIGAR encoded alignments.
(fasta-36.3.4) Alignment option -m B provides BLAST-like alignments (no context, coordinates at the beginning and end of the alignment line, Query/Sbjct.
Improved performance using statistics based thresholds for
gap-joining and band-optimization in the heuristic FASTA local
alignment programs (fasta36, [t]fast[xy]36). By
default (fasta36.3) fasta36, [t]fast[xy]36 can use
a similar strategy to BLAST to set the thresholds for combining
ungapped regions and performing band alignments. This dramatically
reduces the number of band alignments performed, for a speed increase
of 2 - 3X. The original statistical thresholds can be enabled with
the -c O (upper-case letter 'O') command line option.
Protein and translated protein alignment programs can also use ktup=3
for increased speed, though ktup=2 is still the default.
Statistical thresholds can dramatically reduce the number of
"optimized" scores, from which statistical estimates are calculated.
To address this problem, the statistical estimation procedure has
been adjusted to correct for the fraction of scores that were
optimized. This process can dramatically improve statistical accuracy
for some matrices and gap pentalies, e.g. BLOSUM62 -11/-1.
With the new joining thresholds, the
-c "E-opt E-join" options have expanded meanings. -c "E-opt E-join"
calculates a threshold designed (but not guaranteed) to do band
optimization and joining for that fraction of sequences. Thus, -c
"0.02 0.1" seeks to do band optimization (E-opt) on 2% of alignments,
and joining on 10% of alignments. -c "40 10" sets the gap
threshold as in earlier versions.
A new option (-e expand_script.sh) is available that allows
the set of sequences that are aligned to be larger than the set of
sequences searched. When the -e expand_script.sh option is
used, the expand_script.sh script is run with an input
argument that is a file of accession numbers and E()-values; this
information can be used to produce a fasta-formatted list of
additional sequences, which will then be compared and aligned (if they
are significant), and included in the list of high scoring sequences
and the alignments. The expanded set of sequences does not change the
database size o statisical parameters, it simply expands the set of
high-scoring sequences.
The -m F option can be used to produce multiple output formats in different files from the same search. For example, -m "F9c,10 m9c10.output" -m "FBB blastBB.output" produces two output files in addition to the normally formatted output sent to stdout. The m9c10.output file contains -m 9c score descriptions and -m 10 alignments, while blastBB.output contains BLAST-like output (-m BB).
Scoring matrices can vary with query sequence length. In large-scale
searches with metagenomics reads, some reads may be too short to
produce statistically significant scores against comprehensive
databases (e.g. a DNA read of 90 nt is translated into 30 aa, which
would require a scoring matrix with at least 1.3 bits/position to
produce a 40 bit score). fasta-36.3.* includes the option to specify
a "variable" scoring matrix by including '?' as the first letter of
the scoring matrix abbreviation, e.g. fasta36_t -q -s '?BP62' would
use BP62 for sequences long enough to produce significant alignment
scores, but would use scoring matrices with more information content
for shorter sequences. The FASTA programs include BLOSUM50 (0.49
bits/pos) and BLOSUM62 (0.58 bits/pos) but can range to MD10 (3.44
bits/position). The variable scoring matrix option searches down the
list of scoring matrices to find one with information content high
enough to produce a 40 bit alignment score. (Several bugs in the
process are fixed in fasta-36.3.2.)
Several less-used options
(-1, -B, -o, -x, -y) have
become extended options, available via the -X (upper case X) option.
The old -X off1,off2 option is now -o off1,off2.
By default, the program will read up to 2 GB (32-bit systems) or 12 GB
(64-bit systems) of the database into memory for multi-query searches.
The amount of memory available for databases can be set with
the -XM4G option.
Much greater flexibility in specifying combinations of library files
and subsets of libraries. It has always been possible to search a
list of libraries specified by an indirect (@) file; the FASTA36
programs can include indirect files of library names inside of
indirect files of library names.
fasta-36.3.2ggsearch36 (global/global)
and glsearch36 now incorporate SSE2 accelerated global
alignment, developed by Michael Farrar. These programs are now about
20-fold faster.
fasta-36.2.1 (and later versions) are fully threaded, both for
searches, and for alignments. The programs routinely run 12 - 15X
faster on dual quad-core machines with "hyperthreading".
Summary - Major Changes in FASTA version 35 (August, 2007)
Accurate shuffle based statistics for searches of small libraries (or pairwise comparisons).
Inclusion of lalign35 (SIM) into FASTA3. Accurate statistics for
lalign35 alignments. plalign has been replaced by
lalign35 and lav2ps.
Two new global alignment programs: ggsearch35 and glsearch35.
February 7, 2008
Allow annotations in library, as well as
query sequences. Currently, annotations are only available within
sequences (i.e., they are not read from the feature table), but they
should be available in FASTA format, or any of the other ascii text
formats (EMBL/Swissprot, Genbank, PIR/GCG). If annotations are
present in a library and the annotation characters includes '*', then
the -V '*' option MUST be used. However, special characters other
than '*' are ignored, so annotations of '@', '%', or '@' should be
transparent.
In translated sequence comparisons, annotations are only available for
the protein sequence.
January 25, 2007
Support protein queries and sequence
libraries that contain 'O' (pyrrolysine) and 'U' (selenocysteine).
('J' was supported already). Currently, 'O' is mapped automatically to
'K' and 'U' to 'C'.
Dec. 13, 2007 CVS fa35_03_02m
Add ability to search a subset of a library using a file name and a
list of accession/gi numbers. This version introduces a new filetype,
10, which consists of a first line with a target filename, format, and
accession number format-type, and optionally the accession number
format in the database, followed by a list of accession numbers. For
example:
Tells the program that the target database is swissprot.lseg, which is
in FASTA (library type 0) format.
The accession format comes after the ":". Currently, there are four
accession formats, two that require ordered accessions (:1, :2), and
two that hash the accessions (:3, :4) so they do not need to be
ordered. The number and character after the accession format
(e.g. "4|") indicate the offset of the beginning of the accession and
the character that terminates the accession. Thus, in the typical
NCBI Fasta definition line:
The offset is 4 and the termination character is '|'. For databases
distributed in FASTA format from the European Bioinformatics
Institute, the offset depends on the name of the database, e.g.
Accession formats 1 and 3 expect strings; accession formats 2 and 4
work with integers (e.g. gi numbers).
December 10, 2007
Provide encoded annotation information with
-m 9c alignment summaries. The encoded alignment information makes it
much simpler to highlight changes in critical residues.
August 22, 2007
A new program is
available, lav2svg, which creates SVG (Scalable Vector
Graphics) output. In addition, ps_lav,
which was introduced May 30, 2007, has been replaced
by lav2ps. SVG files are more easily edited with Adobe
Illustrator than postscript (lav2ps) files.
July 25, 2007 CVS fa35_02_02
Change default gap penalties for OPTIMA5 matrix to -20/-2 from -24/-4.
July 23, 2007
Add code to support to support sub-sequence ranges for "library"
sequences - necessary for fully functional prss (ssearch35) and
lalign35. For all programs, it is now possible to specify a subset of
both the query and the library, e.g.
lalign35 -q mchu.aa:1-74 mchu.aa:75-148
Note, however, that the subset range applied to the library will be
applied to every sequence in the library - not just the first - and
that the same subset range is applied to each sequence. This probably
makes sense only if the library contains a single sequence (this is
also true for the query sequence file).
July 3, 2007 CVS fa35_02_01
Merge of previous fasta34 with development version fasta35.
June 26, 2007
Add amino-acid 'J' for 'I' or 'L'.
Add Mueller and Vingron (2000) J. Comp. Biol. 7:761-776 VT160 matrix,
"-s VT160", and OPTIMA_5 (Kann et al. (2000) Proteins 41:498-503).
June 7, 2007
ggssearch35(_t), glsearch35(_t) can now use PSSMs.
May 30, 2007 CVS fa35_01_04
Addition of ps_lav
(now lav2ps or lav2svg) -- which can be used to plot the lav
output of
lalign35 -m 11.
lalign35 -m 11 | lav2ps
replaces plalign
(from FASTA2).
May 2, 2007
The labels on the alignment scores are much more informative (and more
diverse). In the past, alignment scores looked like:
where the highlighted text was either: "Smith-Waterman" or "banded
Smith-Waterman". In fact, scores were calculated in other ways,
including global/local for fasts and fastf. With the addition of
ggsearch35,glsearch35, and lalign35, there are many more ways to
calculate alignments: "Smith-Waterman" (ssearch and protein fasta),
"banded Smith-Waterman" (DNA fasta), "Waterman-Eggert",
"trans. Smith-Waterman", "global/local", "trans. global/local",
"global/global (N-W)". The last option is a global global alignment,
but with the affine gap penalties used in the Smith-Waterman
algorithm.
April 19, 2007 CVS fa34t27br_lal_3
Two new programs, ggsearch35(_t) and glsearch35(_t) are now available.
ggsearch35(_t) calculates an alignment score that is global in the
query and global in the library; glsearch35(_t) calculates an alignment
that is global in the query and local, while local in the library
sequence. The latter program is designed for global alignments to domains.
Both programs assume that scores are normally distributed. This
appears to be an excellent approximation for ggsearch35 scores, but
the distribution is somewhat skewed for global/local (glsearch)
scores. ggsearch35(_t) only compares the query to library sequences
that are beween 80% and 125% of the length of the query; glsearch
limits comparisons to library sequences that are longer than 80% of
the query. Initial results suggest that there is relatively little
length dependence of scores over this range (scores go down
dramatically outside these ranges).
March 29, 2007 CVS fa34t27br_lal_1
At last, the lalign (SIM) algorithm has been moved from FASTA21 to
FASTA35. A plalign
equivalent is also available using lalign -m 11 | lav2ps
or | lav2svg.
The statistical estimates for lalign35 should be much more accurate
than those from the earlier lalign, because lambda and K are estimated
from shuffles.
In addition, all programs can now generate accurate statistical
estimates with shuffles if the library has fewer than 500 sequences.
If the library contains more than 500 sequences and the sequences are
related, then the -z 11 option should be used.
pFASTA v34 Change Log
The major improvement in FASTA v36 is the ability to calculate and
display multiple significant alignments (multiple HSP's) between a
query sequence and a library sequence. Previous FASTA versions had
the serious shortcoming of only showing the best
alignment. A tfastx36 alignment between a protein and its
exon-containing gene will show all of the exon alignments that are
long enough to be significant.
FASTA v36 also provides more flexible strategies for searching lists
of datbase files, and versions after fasta-36.2 are fully threaded, so
both searches and alignments can be distributed among multiple
processors with efficient speedup.
PVM/MPI parallel versions of FASTA v36 are under development.
FASTA v35 provides significant improvements in statistical accuracy and program efficiency in threaded (multi-CPU, multi-core) environments. The program now automatically produces 500 random shuffles when small libraries are searched. Thus, prss and prfx are no longer required; ssearch35 and fastx35 provide the same function.
FASTA v34 is the last version of the FASTA3 series before the
significant changes introduced with FASTA v35. The FASTA v3
programs were first introduced in 1996, with threaded code
for multi-processors, more accurate statistical estimates, and
optimal Smith-Waterman alignments with ssearch. More
recent versions (v34) provided accelerated Smith-Waterman searches
using Altivec and SSE2 vector processors. FASTA v34 is no longer
updated for bug fixes.
FASTA v2 was introduced in 1995, improving sensitivity by
calculated gapped alignment scores. Modern (V34 and V35) versions of
FASTA have significantly more robust statistical estimates, threaded
code, and vectorized Smith-Waterman, so FASTA v2 should not be used
for database searching. However, until lalign was addeed
to FASTA v35 in March, 2007, FASTA v2 was the only source for
the lalign program. Today, the only programs provided in
FASTA v2 that are not provided in FASTA v35 are the Kyte-Doolittle
hydropathy plotter grease and the classic (though very
inaccurate) secondary structure prediction programs chofas
and garnier
The current stable version of the FASTA programs is version 35,
and older releases of version 35
are available
to make it easier for software packagers to work with a consistent
version of the software. However,
the CURRENT
version of FASTA should be used whenever possible. Many bug reports
reflect older versions of the software.
Description of minor changes: changes_v35.html
./fasta-36.3.8h/doc/fastf3.1 0000644 0001054 0001054 00000011324 13525131122 012672 0 ustar wrp .TH FASTF/TFASTFv3 1 local
.SH NAME
fastf3, fastf3_t \- compare a mixed peptide sequence against a protein
database using a modified fasta algorithm.
tfastf3, tfastf3_t \- compare a mixed pepide sequence against a
translated DNA database.
.SH DESCRIPTION
.B fastf3
and
.B tfastf3
are designed to compare a sequence of mixed peptides to a protein
(fastf3) or translated DNA (tfastf3) database. Unlike the traditional
.B fasta3
search, which uses a protein or DNA sequence,
.B fastf3
and
.B tfastf3
work with a query sequence of the form:
.in +5
.nf
>testf from mgstm1
MGCEN,
MIDYP,
MLLAY,
MLLGY
.fi
.in 0
This sequence indicates that a mixture of four peptides has been
found, with 'M' in the first position of each one (as from a CNBr
cleavage), in the second position 'G', 'I', or 'L' (twice), at the
third position 'C', 'D', or 'L' (twice), at the fourth position 'E',
'Y', 'A', or 'G', etc. When this sequence is compared against mgstm1.aa
(included with the distribution), the mixture is deconvolved to form:
.nf
.ft C
.in +5
testf MILGY-----------MLLEY-----------MGDAP-----------
::::: ::::: :::::
GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
10 20 30 40 50
testf --------------------------------------------------
GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
60 70 80 90 100
20
testf ------------MLCYN
:::::
GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
110 120 130 140 150
.in 0
.ft P
.fi
.SH Options
.LP
.B fastf3
and
.B tfastf3
can accept a query sequence from the unix "stdin" data stream. This makes it much
easier to use fasta3 and its relatives as part of a WWW page. To
indicate that stdin is to be used, use "-" or "@" as the query
sequence file name.
.TP
\-b #
number of best scores to show (must be < -E cutoff)
.TP
\-d #
number of best alignments to show ( must be < -E cutoff)
.TP
\-D
turn on debugging mode. Enables checks on sequence alphabet that
cause problems with tfastx3, tfasty3, tfasta3.
.TP
\-E #
Expectation value limit for displaying scores and
alignments. Expectation values for
.B fastf3
and
.B tfastf3
are not as accurate as those for the other
.B fasta3
programs.
.TP
\-H
turn off histogram display
.TP
\-i
compare against only the reverse complement of the library sequence.
.TP
\-L
report long sequence description in alignments
.TP
\-m 0,1,2,3,4,5,6,10
alignment display options
.TP
\-n
force query to nucleotide sequence
.TP
\-N #
break long library sequences into blocks of # residues. Useful for
bacterial genomes, which have only one sequence entry. -N 2000 works
well for well for bacterial genomes.
.TP
\-O file
send output to file
.TP
\-q/-Q
quiet option; do not prompt for input
.TP
\-R file
save all scores to statistics file
.TP
\-S #
offset substitution matrix values by a constant #
.TP
\-s name
specify substitution matrix. BLOSUM50 is used by default;
PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120,
P250, or BL62. With this version, many more scoring matrices are
available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10,
M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be
specified.
.TP
\-T #
(threaded, parallel only) number of threads or workers to use (set by
default to 4 at compile time).
.TP
\-t #
Translation table - tfastf3 can use the BLAST tranlation tables. See
\fChttp://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
.TP
\-w #
line width for similarity score, sequence alignment, output.
.TP
\-x "#,#"
offsets query, library sequence for numbering alignments
.TP
\-z #
Specify statistical calculation. Default is -z 1, which uses
regression against the length of the library sequence. -z 0 disables
statistics. -z 2 uses the ln() length correction. -z 3 uses Altschul
and Gish's statistical estimates for specific protein BLOSUM scoring
matrices and gap penalties. -z 4: an alternate regression method.
.TP
\-Z db_size
Set the apparent database size used for expectation value calculations.
.TP
\-1
Sort by "init1" score.
.TP
\-3
(TFASTF3 only) use only forward frame translations
.SH Environment variables:
.TP
FASTLIBS
location of library choice file (-l FASTLIBS)
.TP
SMATRIX
default scoring matrix (-s SMATRIX)
.TP
SRCH_URL
the format string used to define the option to re-search the
database.
.TP
REF_URL
the format string used to define the option to lookup the library
sequence in entrez, or some other database.
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU
./fasta-36.3.8h/doc/fasts3.1 0000644 0001054 0001054 00000010710 13525131122 012705 0 ustar wrp .TH FASTS/TFASTSv3 1 local
.SH NAME
fasts3, fasts3_t \- compare several short peptide sequences against a protein
database using a modified fasta algorithm.
tfasts3, tfasts3_t \- compare short pepides against a
translated DNA database.
.SH DESCRIPTION
.B fasts3
and
.B tfasts3
are designed to compare set of (presumably non-contiguous) peptides to
a protein (fasts3) or translated DNA (tfasts3) database.
fasts3/tfasts3 are designed particularly for short peptide data from
mass-spec analysis of protein digests. Unlike the traditional
.B fasta3
search, which uses a protein or DNA sequence,
.B fasts3
and
.B tfasts3
work with a query sequence of the form:
.in +5
.nf
>tests from mgstm1
MLLE,
MILGYW,
MGADP,
MLCYNP
.fi
.in 0
This sequence indicates that four peptides are to be used. When this
sequence is compared against mgstm1.aa (included with the
distribution), the result is:
.nf
.ft C
.in +5
testf MILGYW----------MLLE------------MGDAP-----------
:::::: :::: :::::
GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
10 20 30 40 50
testf --------------------------------------------------
GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
60 70 80 90 100
20
testf ------------MLCYNP
::::::
GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
110 120 130 140 150
.in 0
.ft P
.fi
.SH Options
.LP
.B fasts3
and
.B tfasts3
can accept a query sequence from the unix "stdin" data stream. This makes it much
easier to use fasta3 and its relatives as part of a WWW page. To
indicate that stdin is to be used, use "-" or "@" as the query
sequence file name.
.TP
\-b #
number of best scores to show (must be < -E cutoff)
.TP
\-d #
number of best alignments to show ( must be < -E cutoff)
.TP
\-D
turn on debugging mode. Enables checks on sequence alphabet that
cause problems with tfastx3, tfasty3, tfasta3.
.TP
\-E #
Expectation value limit for displaying scores and
alignments. Expectation values for
.B fasts3
and
.B tfasts3
are not as accurate as those for the other
.B fasta3
programs.
.TP
\-H
turn off histogram display
.TP
\-i
compare against only the reverse complement of the library sequence.
.TP
\-L
report long sequence description in alignments
.TP
\-m 0,1,2,3,4,5,6,9,10
alignment display options
.TP
\-N #
break long library sequences into blocks of # residues. Useful for
bacterial genomes, which have only one sequence entry. -N 2000 works
well for well for bacterial genomes.
.TP
\-O file
send output to file
.TP
\-q/-Q
quiet option; do not prompt for input
.TP
\-R file
save all scores to statistics file
.TP
\-S #
offset substitution matrix values by a constant #
.TP
\-s name
specify substitution matrix. BLOSUM50 is used by default;
PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120,
P250, or BL62. With this version, many more scoring matrices are
available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10,
M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be
specified.
.TP
\-T #
(threaded, parallel only) number of threads or workers to use (set by
default to 4 at compile time).
.TP
\-t #
Translation table - tfasts3 can use the BLAST tranlation tables. See
\fChttp://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
.TP
\-w #
line width for similarity score, sequence alignment, output.
.TP
\-x "#,#"
offsets query, library sequence for numbering alignments
.TP
\-z #
Specify statistical calculation. Default is -z 1, which uses
regression against the length of the library sequence. -z 0 disables
statistics. -z 2 uses the ln() length correction. -z 3 uses Altschul
and Gish's statistical estimates for specific protein BLOSUM scoring
matrices and gap penalties. -z 4: an alternate regression method.
.TP
\-Z db_size
Set the apparent database size used for expectation value calculations.
.TP
\-3
(TFASTS3 only) use only forward frame translations
.SH Environment variables:
.TP
FASTLIBS
location of library choice file (-l FASTLIBS)
.TP
SMATRIX
default scoring matrix (-s SMATRIX)
.TP
SRCH_URL
the format string used to define the option to re-search the
database.
.TP
REF_URL
the format string used to define the option to lookup the library
sequence in entrez, or some other database.
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU
./fasta-36.3.8h/doc/map_db.1 0000644 0001054 0001054 00000001664 13525131122 012734 0 ustar wrp .TH MAP_DB "September, 1999"
.SH NAME
.B map_db
\- read a FASTA (0), GENBANK flat file (1) PIR/VMS (5) or GCG binary
(6) sequence database and produce the offsets necessary for efficient
memory mapping.
.SH SYNOPSIS
.B map_db
[-n] filename | "filename libtype"
.SH DESCRIPTION
.B map_db
.I filename
reads the sequence database in
.I filename
and produce a new file
.I filename.xin
with the offset information necessary for efficient memory mapping.
.LP
The programs in fasta version 32t08 can use memory mapped i/o to load
sequence database files and read them efficiently. Memory mapping is
used only if a "\c
.I .xin\c
\&" file is available. The "\c
.I .xin\c
\&" file is created by
.B map_db\c
\&.
.LP
In addition to
.B map_db\c
\&,
.B list_db
is available to display the database size, etc, and set of offsets calculated
by
.B map_db\c
\&.
.SH OPTIONS
.TP
\-n
Read file as DNA database.
.SH BUGS
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU
./fasta-36.3.8h/doc/prss3.1 0000644 0001054 0001054 00000011551 13525131122 012560 0 ustar wrp .TH PRSS3 1 local
.SH NAME
prss \- test a protein sequence similarity for significance
.SH SYNOPSIS
.B prss34
\&[-Q -A -f # -g # -H -O file -s SMATRIX -w # -Z #
.I -k # -v #
]
sequence-file-1 sequence-file-2
[
.I #-of-shuffles
]
.B prfx34
\&[-Q -A -f # -g # -H -O file -s SMATRIX -w # -z 1,3 -Z #
.I -k # -v #
]
sequence-file-1 sequence-file-2
[
.I ktup
]
[
.I #-of-shuffles
]
.B prss34(_t)/prfx34(_t)
[-AfghksvwzZ]
\- interactive mode
.SH DESCRIPTION
.B prss34
and
.B prfx34
are used to evaluate the significance of a protein:protein, DNA:DNA
(
.B prss34
), or translated-DNA:protein (
.B prfx34
) sequence similarity score
by comparing two sequences and calculating optimal similarity scores,
and then repeatedly shuffling the second sequence, and calculating
optimal similarity scores using the Smith-Waterman algorithm. An
extreme value distribution is then fit to the shuffled-sequence
scores. The characteristic parameters of the extreme value
distribution are then used to estimate the probability that each of
the unshuffled sequence scores would be obtained by chance in one
sequence, or in a number of sequences equal to the number of shuffles.
This program is derived from
.B rdf2\c
\&, described by Pearson and Lipman, PNAS (1988) 85:2444-2448, and
Pearson (Meth. Enz. 183:63-98). Use of the extreme value
distribution for estimating the probabilities of similarity scores was
described by Altshul and Karlin, PNAS (1990) 87:2264-2268. The
'z-values' calculated by rdf2 are not as informative as the P-values
and expectations calculated by prdf.
.B prss34
calculates optimal scores using the same rigorous Smith-Waterman
algorithm (Smith and Waterman, J. Mol. Biol. (1983) 147:195-197) used by the
.B ssearch34
program.
.B prfx34
calculates scores using the FASTX algorithm (Pearson et al. (1997) Genomics 46:24-36.
.PP
.B prss34
and
.B prfx34
also allow a more sophisticated shuffling method: residues can be shuffled
within a local window, so that the order of residues 1-10, 11-20, etc,
is destroyed but a residue in the first 10 is never swapped with a residue
outside the first ten, and so on for each local window.
.SH EXAMPLES
.TP
(1)
.B prss34
\& -v 10 musplfm.aa lcbo.aa
.PP
Compare the amino acid sequence in the file musplfm.aa with that
in lcbo.aa, then shuffle lcbo.aa 200 times using a local shuffle with
a window of 10. Report the significance of the
unshuffled musplfm/lcbo comparison scores with respect to the shuffled
scores.
.TP
(2)
.B prss34
musplfm.aa lcbo.aa 1000
.PP
Compare the amino acid sequence in the file musplfm.aa with the sequences
in the file lcbo.aa, shuffling \fClcbo.aa\fP 1000 times. Shuffles can also be specified with the -k # option.
.TP
(3)
.B prfx34
mgstm1.esq xurt8c.aa 2 1000
.PP
Translate the DNA sequence in the \fCmgstm1.esq\fP file in all six
frames and compare it to the amino acid sequence in the file
\fCxurt8c.aa\fP, using ktup=2 and shuffling \fCxurt8c.aa\fP 1000
times. Each comparison considers the best forward or reverse
alignment with frameshifts, using the fastx algorithm (Pearson et al
(1997) Genomics 46:24-36).
.TP
(4)
.B prss34/prfx34
.PP
Run prss in interactive mode. The program will prompt for the file
name of the two query sequence files and the number of shuffles to be
used.
.SH OPTIONS
.PP
.B prss34/prfx34
can be directed to change the scoring matrix, gap penalties, and
shuffle parameters by entering options on the command line (preceeded
by a `\-'). All of the options should preceed the file names number of
shuffles.
.TP
\-A
Show unshuffled alignment.
.TP
\-f #
Penalty for opening a gap (-10 by default for proteins).
.TP
\-g #
Penalty for additional residues in a gap (-2 by default) for proteins.
.TP
\-H
Do not display histogram of similarity scores.
.TP
\-k #
Number of shuffles (200 is the default)
.TP
\-Q -q
"quiet" - do not prompt for filename.
.TP
\-O filename
send copy of results to "filename."
.TP
\-s str
specify the scoring matrix. BLOSUM50 is used by default for proteins;
+5/-4 is used by defaul for DNA.
.B prss34
recognizes the same scoring matrices as fasta34, ssearch34, fastx34, etc;
e.g. BL50, P250, BL62, BL80, MD10, MD20, and other matrices in BLAST1.4
matrix format.
.TP
\-v #
Use a local window shuffle with a window size of #.
.TP
\-z #
Calculate statistical significance using the mean/variance
(moments) approach used by fasta34/ssearch or from maximum likelihood
estimates of lambda and K.
.TP
\-Z #
Present statistical significance as if a '#' entry database had
been searched (e.g. "-Z 50000" presents statistical significance as if
50,000 sequences had been compared).
.SH ENVIRONMENT VARIABLES
.PP
.B (SMATRIX)
the filename of an alternative scoring matrix file. For protein
sequences, BLOSUM50 is used by default; PAM250 can be used with the
command line option
.B -s P250\c
(or with -s pam250.mat). BLOSUM62 (-s BL62) and PAM120 (-S P120).
.SH "SEE ALSO"
ssearch3(1), fasta3(1).
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU
./fasta-36.3.8h/doc/ps_lav.1 0000644 0001054 0001054 00000001205 13525131122 012765 0 ustar wrp .TH PS_LAV 1 local
.SH NAME
ps_lav [-B] [-Z db_size] \- plot an "lav" file in postscript.
.SH DESCRIPTION
ps_lav is a simple program to take "lav" format output from "lalign35"
and produce postscript alignment plots (which look like "dot-plots").
It was designed to work with the output of the \fClalign35\fP program,
but should work with other \fClav\fP output as well.
.TP
\-B
color alignment lines using the "bit" score.
.TP
\-Z db_size
set the effective database size for an E()-value calculate to db_size,
and color alignment lines using E()-values. Requires bit scores in
the \fClav\fP ouput.
.SH AUTHOR
Bill Pearson
.br
wrp@virginia.EDU
./fasta-36.3.8h/doc/readme.md 0000777 0001054 0001054 00000000000 13525131122 015631 2README_v36.3.8h.md ustar wrp ./fasta-36.3.8h/doc/readme.v30 0000644 0001054 0001054 00000002056 13525131122 013213 0 ustar wrp
Because of interdependencies in the Makefile, sometimes you must
type "make" a second time to get everything built.
June 12, 1996 - fasta30t1
Fixed bug in reading blast-format DNA sequence files.
Fixed core-dump for some large libraries on some machines.
June 19, 1996 - fasta30t2
Fixed a serious bug in the Smith-Waterman alignment routines used
by both fasta3 (dropnfa.c) and ssearch3 (dropgsw.c) that caused
the amount of memory required to depend on the library sequence
size, rather than the query sequence size.
Fixed some memory-overwrite errors in showalign.c
June 27, 1996 - fasta30t3
Found and fixed bugs in comp_thr.c and nxgetaa.c that caused core
dumps when reading DNA libraries with long sequences in fasta
format.
July 6, 1996 - fasta30t4
ibm_pthread_subs.c available, Makefile.ibm for multiprocessor
IBM RS/6000 AIX systems.
Finally (?) fixed the previous bug that caused core dumps when
reading DNA libraries in fasta format.
Corrections to the fastx algorithm.
July 10, 1996
Fixed reading of compressed GCG DNA format.
./fasta-36.3.8h/doc/readme.v30t6 0000644 0001054 0001054 00000003517 13525131122 013470 0 ustar wrp
>>August 24, 1996
New programs - tfastx3, tfastx3_t, compare a protein sequence to
forward and reverse translations of a DNA sequence database. An excellent
replacement for tfasta3.
Sun multiprocessing - change in thr_create() to use all CPU's if available.
GCG formats - now can search with simple GCG-format query sequences and
results with GCG format Swissprot and Genpept are more readable.
>>August 26, 1996
Fixed bugs in tfastx3(_t) and fastx3(_t) including an ancient problem
with aatran(). Less redundancy in gcg_ranlib().
>>August 31, 1996
Included support for BLOSUM62 (-s BL62) as per documentation.
Rearranged Makefile's so that they would make everything in one pass.
>>September 6, 1996
Corrected yet another problem with the fastx/tfastx code.
Noticed that searching without optimized scores gave no optimized
scores on the final list of scores - fixed this.
The pvm version now does alignments - not thoroughly tested.
>>September 13, 1996
Fixed display of best scores to stdout.
Fixed problem with alignments when -o flag used.
pvcompfa/pvcompsw have now been tested on DEC Alpha, Solaris X86, and
SGI PVM implementations. Several bugs were corrected.
>>September 18, 1996
Fixed bug selectbestz() that caused core dumps in pvcomplib.c
(changes to pvcomplib.c, comp_thr.c, complib.c).
>>September 23, 1996
Corrected showalign.c/pvm_showalign.c addressing bug found and fixed
by Erik Wallin. (erikw@biokemi.su.se).
>>October 15, 1996
Corrected bug so alternative scoring matrices are used.
>>October 22, 1996
Remove singularities from regression routine.
-z 0 now means no statistics (same as -z -1).
No longer show alignment for 0 score.
>>October 26, 1996
Fix problem with -b, -d when Z-values disabled.
>>November 1, 1996
Altschul-Gish statistical estimates (-z 3) now work properly.
Fix problem with mean_var==0.0.
./fasta-36.3.8h/doc/readme.v30t7 0000644 0001054 0001054 00000012243 13525131122 013465 0 ustar wrp >> October 30, 1996
A new program, sc_to_e, can be used to calculate expectation values
from the regression coefficients reported from a search. The
expectation value is based on similarity score, sequence length, and
database size.
>> November 8, 1996
fasta30t7 differs from fasta30t6 in the amount of information provided
with the -m 10 option.
(1) The query and library sequence identifiers are no longer abbreviated.
(2) New information about the program and program version are provided:
The new information provided is:
mp_name: program name (actually argv[0])
mp_ver: main program version (can be different from function version)
mp_argv: command line arguments (duplicates argv[0])
Some statistical information is provided as well:
mp_extrap: XXXX YYY - statistics extrapolated from XXX to YYY
mp_stats: indicates type of statistics used for E() value
mp_KS: Kolmogorov-Smirnoff statistic
The "mp_" (main program) information is function independent, while the "pg_"
information is produced by a particular comparison function (ssearch,
fastx, fasta, etc). "pg_" should probably be called "fn_", and "mp_"
called "pg_", but I remain backwards compatible.
(3) The end of the "parseable" records is denoted with:
>>><<<
(4) There now an compile-time option -DM10_CONS, that allows you to
display a final alignment summary:
;al_cons:
.::.:- .:: .. :. .:.---: : .--.:. :
.. .--- ..: :: ... :..: .::.:. . .---. . .:
: . . . : .. . :..: .--. . : .:. .. : .
.:.::: ..:. :
or, if M10_CONS_L is defined (in addition to M10_CONS), the output is:
;al_cons:
p==p=-mmmp==mpzmm=pmmmmz=p---=mmm=mmp--p=zm=m
pzmmp---mmzp=m==mzzzm=zp=mz==z=pmzmmz---pmmpmmmp=m
m=mzmmzmpm=mmmmppmmmpmmmm=pp=mp--pmpm=mp=pmzzm=mmp
mp=z===mmpz=zm=
where '=' indicates identical residues, '-' a gap in one or the other
sequence, 'p' indicates a positive pam value, 'm' indicates a negative
pam value, and 'z' indicates a zero pam value.
A typical run now looks like:
>>>gtm1_mouse.aa, 217 aa vs s library
; mp_name: fasta3_t
; mp_ver: version 3.0t7 November, 1996
; mp_argv: fasta3_t -q -m 10 gtm1_mouse.aa s
; pg_name: FASTA
; pg_ver: 3.06 Sept, 1996
; pg_matrix: BL50
; pg_gap-pen: -12 -2
; pg_ktup: 2
; pg_optcut: 24
; pg_cgap: 36
; mp_extrap: 50000 51933
; mp_stats: Expectation fit: rho(ln(x))= 5.8855+/-0.000527; mu= 1.5386+/- 0.029; mean_var=73.0398+/-15.283
; mp_KS: 0.0133 (N=29) at 42
>>GTM1_MOUSE GLUTATHIONE S-TRANSFERASE GT8.7 (EC 2.5.1.18) (GST 1-1) (CLASS-MU).
; fa_initn: 1490
; fa_init1: 1490
; fa_opt: 1490
; fa_z-score: 1754.6
; fa_expect: 0
; sw_score: 1490
; sw_ident: 1.000
; sw_overlap: 217
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>>GTM1_RAT GLUTATHIONE S-TRANSFERASE YB1 (EC 2.5.1.18) (CHAIN 3) (CLASS-MU).
; fa_initn: 1406
; fa_init1: 1406
; fa_opt: 1406
; fa_z-score: 1656.3
; fa_expect: 0
; sw_score: 1406
; sw_ident: 0.931
; sw_overlap: 217
>GTM1_MOUSE ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKF
KLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVE
NQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS
RYIATPIFSKMAHWSNK
>GTM1_RAT ..
; sq_len: 217
; sq_type: p
; al_start: 1
; al_stop: 217
; al_display_start: 1
PMILGYWNVRGLTHPIRLLLEYTDSSYEEKRYAMGDAPDYDRSQWLNEKF
KLGLDFPNLPYLIDGSRKITQSNAIMRYLARKHHLCGETEEERIRADIVE
NQVMDNRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGD
KVTYVDFLAYDILDQYHIFEPKCLDAFPNLKDFLARFEGLKKISAYMKSS
RYLSTPIFSKLAQWSNK
;al_cons:
:::::::::::::::::.:::::::::.::::.::::::.::::::::::
::::::::::::::::.::::::::.::::::::: ::::::::::::::
:::::.::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::..::::::::::::.:::::::::::::::::::
::..::::::.:.::::
>>><<<
217 residues in 1 query sequences
18531385 residues in 52205 library sequences
Tcomplib (4 proc)[version 3.0t7 November, 1996]
start: Fri Nov 8 18:20:26 1996 done: Fri Nov 8 18:20:41 1996
Scan time: 38.434 Display time: 2.166
Function used was FASTA
================================================================
>> November 11, 1996
--> v30t71
Made changes to complib.c, comp_thr.c, nxgetaa.c to allow scoring
matrix to be modified in fastx3, fastx3_t.
================================================================
>> November 15, 1996
--> v30t72
nxgetaa.c now accepts query sequences from "stdin" by using "-" as the
input file name. If DNA sequences are read in this mode, the "-n"
option must be used.
> November 23, 1996
Included code in nxgetaa.c and Makefile.sgi to get around a bug in SGI's
sscanf() that prevented compressed GCG databases from being read properly.
./fasta-36.3.8h/doc/readme.v31t0 0000644 0001054 0001054 00000010555 13525131122 013463 0 ustar wrp
>>November 1, 1997
--> v31t0
version 31t of the fasta program package uses a more modular
structure for comparison functions. In addition to modular functions
to initialize, calculate and align sequences, v31 provides a modular
function for creating the alignment display. This was required for
fasty and fastf, which have very different alignment strategies from
the other search programs.
>>February 13, 1998
modified nascii[] so that 0, 1, 2 are no longer end of sequence
characters.
prss3 added. Unlike prss, prss3 uses -d # to specify the number of
shuffles.
>>March 18, 1998
First public release. Corrected problems with dropfz.c (which is
used in fasty3, tfasty3). Makefile is well tested, but other Makefile's
are not. PVM versions not tested.
>>March 19, 1998
Problem with unthreaded tfastx3, tfasty3 caused by bug in complib.c
fixed. All Makefiles (Makefile.alpha Makefile.sun, Makefile.sgi,
Makefile.linux) have been tested and work properly. Threaded versions
do not work on linux (yet). Function labeling problems with fasty3,
tfasty3 corrected.
>>March 20, 1998
--> v31t02
Fixed problem with inconsistent openlib() calls that broke BLAST databases
on some platforms.
>>March 27, 1998
--> v31t04
Fixed a long standing problem with fastx/tfastx and fasty/tfasty that
caused various memory allocation problems and core dumps.
The PVM version works again, but cannot produce alignments. The
change in the location of the modular display functions will require
significant changes in the pvm display functions. For the moment,
showalign() has been commented out.
Code tested on Macintosh without changes.
Added some additional information in the results file.
Please report bugs to wrp@virginia.edu
>>April 3, 1998
Removed some debugging code in faatran.c now that fastx/fasty bugs
seem corrected.
FASTA --> v3.14
Corrected uninitialized array elements in dropnfa.c.
>>April 10, 1998
Added facility for specifying SRCH_URL (the URL string that will be
used to re-search the database) and REF_RUL (the URL string that
will be used to lookup the sequence) ini url_subs.c. This allows perl
scripts to provide different databases for re-searching dynamically.
>>April 16, 1998
--> v31t05
Corrected problem with ignoring ','s in databases (','s are found in
PIR).
>>April 18, 1998
Corrected some problems with sequence names for Entrez lookups and
re-searching databases.
Made minor modifications to nxgetaa.c and compacc.c for compatibility
with Borland 'C' compiler for Win32 systems. Including makefile.tc
fasta.rsp, prss.rsp, and test.bat for Borland 'C'/win32.
>>April 24, 1998
--> v31t06
Fixed another bug in fasty3/tfasty3 alignment routines.
Added additional information to the do_url1() (url_subs.c) function.
The re-search URL can now reference the start, stop, and length of the
library sequence to be re-searched with. For DNA library sequences,
these values are always in nucleotides, even with tfasta/x/y.
>>May 12, 1998
(no version change as v31t06 was not released prior to this)
Correct nxgetaa.c GETLIB to deal correctly with BLAST NR database
sequences with exceptionally long title lines.
Fix bug with long -O results files.
>>May 18, 1998
--> v31t07
Corrected some bugs in information string lengths (e.g. gstring1,
stat_str), disabling statistics with -z 0, translation of 'X' by
saatran() (faatran.c) that caused problems with FASTX.
A serious bug has been fixed in the FASTX alignment routines.
For some pathological sequences, % identity increases from < 10%
to 40%. The version number of the main program has not changed,
but the version number of the fastx function has changed to 3.2.
>>June 19, 1998
--> v31t08
Corrected some problems with alignments with -m 10.
Added -Z db_size option to modify apparent database size for
expectation value calculation (used only for protein/protein FASTA and
SSEARCH, FASTX, FASTY, TFASTX, and TFASTY).
>>July 1, 1998
(no version change)
Corrected size of lbnames[], lb_size[] in structs.h to accomodate MAX_LF
files.
>>July 13, 1998
--> v31t09
Corrected problem in nxgetaa.c encountered when reading long sequences
(that must be split) in fasta format.
Corrected problem in statistics calculation encountered with a small number
of very long DNA sequences.
>>July 17, 1998
(no version change, date change for ssearch3)
Corrected default expectation cutoff (it was 10, now it is 2.0) for
DNA with ssearch3.
./fasta-36.3.8h/doc/readme.v31t1 0000644 0001054 0001054 00000007060 13525131122 013461 0 ustar wrp >>July 22, 1998
--> v31t10
Corrected problem with histogram when unscaled statistics used (e.g. prss3).
Corrected problems with prss3 shuffled sequence prompt. Provided option
to enter number of shuffles, window size, for prss3. Number of shuffles
for prss3 can be entered as an option (-d #) or as the third argument
on the command line (prss3 query lib 1000).
Modified nrand.c, nrand48.c to use time to set random number.
Corrected problems reading GCG formatted files with prss3.
Corrected various problems with pvcomp* programs, but they still do
not produce alignments with version 3.1.
Two new programs, fastf3(_t) and tfastf3(_t) are available. These
programs compare a set of mixed peptide sequences from an Edman
sequencer to a protein (fastf3) or DNA (tfastf3) database, using
the database sequences to de-convolve the peptide mixture.
See fastf3.1
>>August 11, 1998
(no version change)
Modified initfa.c so that using '-n' on the fastx/fasty command line
would not cause problems.
Changed labeling of query sequence length for fastx/fasty from 'aa' to 'nt'.
>>August 18, 1998
(no version change)
Modified complib.c, comp_thr.c scaleswn.c, to report E()-value for only
one related sequence if -z 3 is used.
>>August 23, 1998
-->v31t11
Some serious problems with prss3 have been corrected:
(1) use dropnsw.c rather than dropgsw.c for more accurate low scores
(2) modify estimation program; use scaleswe.c rather than scaleswn.c.
scaleswe.c has some improvements for estimation by moments and can
use MLE as well as mu/var (-z 3).
(3) add p() estimate.
(4) correct bugs in nrand48, which caused bad sequences for llgetaa.c
(5) -Z number works properly for prss3 and other programs (fixed histogram).
(6) a new program, ssearch3e, is available that uses the same scaling
routines as prss3 (scaleswe.c). prss3 will save the random
sequences it generates when the -r file option is given; the
sequences are in file_rlib. ssearch3e (or ssearch3 or fasta) can
then do a search on exactly the same sequences that were used by prss3.
A bug reading GCG format compressed DNA databases was fixed.
Fixed a bug that caused query sequence not to be displayed with -m 10.
Simple optimization in dropnfa.c improves performance 10%.
>>Sept. 1, 1998
(no version change)
Modified nxgetaa.c to recognize "ACGTX" as nucleotides.
>>Sept. 7, 1998
--> v31t12
Added -z 11 - 15, which use shuffled sequences, rather than real
sequences to calculate statistical estimates. Because a shuffled
sequence score is calculated for each sequence score, the search
process takes twice as long. In this first version, codons are not
preserved during shuffles, so tfasta/x/y shuffles may not be as
informative as they should be.
Also fix a problem with prss3 shuffles.
>>Sept. 14, 1998
(no version change; previous version not released)
Corrected bugs in tfastx3/tfasty3 caused by using the -3 option with
or without -i. With the bug fixes; "-3" and "-3 -i" work as expected;
"-3" gives the forward three frames, while "-3 -i" gives the reverse
three frames.
In addition, tfasta3/tfasta3_t was upgraded to perform the same way
that tfastx/y3 does - i.e. a search with "-i -3" searches only frames
4,5, and 6, while "-3" searches only frames 1, 2, and 3.
>>Sept. 29, 1998
--> v31t13
Corrected bugs in dropfx.c that were corrected in fasta30 last May,
but lingered in fasta31. Also included code to ensure that tfastx/y
alignments against long introns would not overrun the alignment
buffer. Instead of overrunning the buffer, the message: ***aligment
truncated *** is displayed.
./fasta-36.3.8h/doc/readme.v32t0 0000644 0001054 0001054 00000036741 13525131122 013471 0 ustar wrp
FASTX/Y and FASTA (DNA) are now half as fast, because the programs now
search both the forward and reverse strands by default.
The documentation in fasta3x.me/fasta3x.doc has been substantially
revised.
>>October 9, 1999
--> v32t08 (no version number change)
Added "-M low-high" option, where low and high are inclusion limits
for library sequences. If a library sequence is shorter than "low" or
longer than "high", it will not be considered in the search. Thus,
"-M 200-250" limits the database search to proteins between 200 and
250 residues in length. This should be particularly useful for fasts3
and fastf3. This limit applies only to protein sequences.
Modified scaleswn.c to fall back to maximum likelihood estimates of
lambda, K rather than mean/variance estimates. (This allows MLE
estimation to be used instead of proc_hist_n when a limited range of
scores is examined.)
>>October 20, 1999
(no version change)
Modify nxgetaa.c/nmgetaa.c to recognize 'N' as a possible DNA character.
>>October 9, 1999
--> v32t08 (no version number change)
Added "-M low-high" option, where low and high are inclusion limits
for library sequences. If a library sequence is shorter than "low" or
longer than "high", it will not be considered in the search. Thus,
"-M 200-250" limits the database search to proteins between 200 and
250 residues in length. This should be particularly useful for fasts3
and fastf3. -M -500 searches library sequences < 500; -M 200 -
searches sequences > 200. This limit applies only to protein
sequences.
Modified scaleswn.c to fall back to maximum likelihood estimates of
lambda, K rather than mean/variance estimates. (This allows MLE
estimation to be used instead of proc_hist_n when a limited range of
scores is examined.)
>>October 2, 1999
--> v32t08
Many changes:
(1) memory mapped (mmap()ed) database reading - other database reading fixes
(2) BLAST2 databases supported
(3) true maximum likelihood estimates for Lambda, K
(4) Misc. minor fixes
(1) (Sept. 26 - Oct. 2, 1999) Memory mapped database access.
It is now possible to use mmap()ed access to FASTA format databases,
if the "map_db" program has been used to produce an ".xin" file. If
USE_MMAP is defined at compile time and a ".xin" file is present, the
".xin" will be used to access sequences directly after the file is
mmap()ed. On my 4-processor Alpha, this can reduce elapsed time by
50%. It is not quite as efficient as BLAST2 format, but it is close.
Currently, memory mapping is supported for type 0 (FASTA), 5
(PIR/GCG ascii), and 6 (GCG binary). Memory mapping is used if a
".xin" file is present. ".xin" files are created by the new program
"map_db". The syntax for "map_db" is:
map_db [-n] "/dir/database.fa"
which creates the file /dir/database.fa.xin. Library types can be
included in the filename; thus:
map_db -n "/gcggenbank/gb_om.seq 6"
would be used for a type 6 GCG binary file.
The ".xin" file must be updated each time the database file changes.
map_db writes the size of the database file into the ".xin" file, so
that if the database file changes, making the ".xin" offset
information invalid, the ".xin" file is not used. "list_db" is
provided to print out the offset information in the ".xin" file.
(Oct 2, 1999) The memory mapping routines have been changed to
allow several files to be memory mapped simultaneously. Indeed, once a
database has been memory mapped, it will not be unmap()ed until the
program finishes. This fixes a problem under Digital Unix, and should
make re-access to mmap()ed files (as when displaying high scores and
alignments) much more efficient. If no more memory is available for
mmap()ing, the file will be read using conventional fread/fgets.
(Oct 2, 1999) The names of the database reading functions has been
changed to allow both Blast1.4 and Blast2.0 databases to be read. In
addition, Makefile.common now includes an option to link both
ncbl_lib.o and ncbl2_lib.o, which provides support for both libraries.
However, Blast1.4 support has not been tested.
The Makefile structure has been improved. Each architecture specific
Makefile (Makefile.alpha, Makefile.linux, etc) now includes
Makefile.common. Thus, changes to the program structure should be
correct for all platforms. "map_db" and "list_db" are not made with
"make all".
The database reading functions in nxgetaa.c can now return a database
length of 0, which indicates that no residues were read. Previously,
0-length sequences returned a length of 1, which were ignored.
Complib.c and comp_thr.c have changed to accommodate this
modification. This change was made to ensure that each residue,
including the last, of each sequence is read.
Corrected bug in nxgetaa.c with FASTA format files with very long
(>512 char) definition lines.
(2) (September 20, 1999) BLAST2 format databases supported
This release supports NCBI Blast2.0 format databases, using either
conventional file reading or memory mapped files. The Blast2.0 format
can be read very efficiently, so there is only a modest improvement in
performance with memory mapping. The decision to use mmap()'ed files
is made at compile time, by defining USE_MMAP. My thanks to Eamonn
O'Toole of DEC/Compaq, and Daryl Madura of Sun Microsystems, for
providing mmap()'ed modifications to fasta3. On my machines, Blast2.0
format reduces search time by about 30%. At the moment, ambiguous DNA
sequences are not decoded properly.
(3) (September 30, 1999) A new statistical estimation option is
available. -z 2 has been changed from ln()-scaling, which never
should have been used, to scaling using Maximum Likelihood Estimates
(MLEs) of Lambda and K. The MLE estimation routines were written by
Aaron Mackey, based on a discussion of MLE estimates of Lambda and K
written by Sean Eddy. The MLE estimation examines the middle 95% of
scores, if there are fewer than 10000 sequences in the database;
otherwise it excludes (censors) the top 250 scores and the bottom 250
scores. This approach seems to effectively prevent related sequences
from contaminating the estimation process. As with -z 1, -z 12 causes
the program to generate a shuffled sequence score for each of the
library sequences; in this case, no censoring is done. If the
estimation process is reliable, Lambda and K should not vary much with
different queries or query lengths. Lambda appears not to vary much
with the comparison algorithm, although K does.
(4) Minor changes include fixes to some of the alignment display routines,
individual copies of the pstruct structure for each thread, and some
changes to ensure that every last residue in a library is available
for matching (sometime the last residue could be ignored). This
version has undergone extensive testing with high-throughput sequences
to confirm that long sequences are read properly. Problems with
fastf3/fasts3 alignment display have also been addressed.
>>August 26, 1999 (no version change - not released)
Corrected problem in "apam.c" that prevented scoring matrices from
being imported for [t]fasts3/[t]fastf3.
>>August 17, 1999
--> v32t07
Corrected problem with opt_cut initialization that only appeared
with pvcomp* programs.
Improved calculation of FASTA optcut threshold for DNA sequence
comparison for match scores much less than +5 (e.g. +3). The previous
optcut theshold was too high when the match penalty was < 4 and
ktup=6; it is now scaled more appropriately.
Optcut thresholds have also been raised slightly for
fastx/y3/tfastx/y3. This should improve performance with minimal
effects on sensitivity.
>>July 29, 1999
(no version change - date change)
Corrected various uninitialized variables and buffer overruns
detected.
>>July 26, 1999 - new distribution
(no version change - v32t06, previous version not released)
Changed the location of "(reverse complement)" label in tfasta/x/y/s/f
programs.
Statistical calculations for tfasta/x/y in unthreaded version
corrected. Statistical estimates for threaded and unthreaded versions
of the tfasta/x/y/s/f programs should be much more consistent.
Substantial modifications in alignment coordinate calculation/
presentation. Minor error in fastx/y/tfastx/y end of alignment
corrected. Major problems with tfasta alignment coordinates
corrected. tfasta and tfastx/y coordinates should now be consistent.
Corrected problem with -N 5000 in tfasta/x/y3(_t) searches encountered
with long query sequences.
Updated pthr_subs.c/Makefile.linux to increase the pthreads stacksize
to try to avoid "cannot allocate diagonal arrays" error message.
Pthreads stacksize can be changed with RedHat 6.0, but not RedHat 5.2,
so Makefile.linux uses -DLINUX5 for RedHat5.* (no pthreads stack size).
I am still getting this message, so it has not been completely
successful. Makefile.linux now uses -DALLOCN0 to avoid this problem,
at some cost in speed.
The pvcomp* programs have been updated to work properly with
forward/reverse DNA searches. See readme.pvm_3.2.
>>July 7, 1999 - not released
--> v32t06
Corrected bug in complib.c (fasta3, fastx3, etc) that caused core
dumps with "-o" option.
Corrected a subtle bug in fastx/y/tfastx/y alignment display.
>>June 30, 1999 - new distribution
(no version change)
Corrected doinit.c to allow DNA substitution matrices with -s matrix
option.
Changed ".gbl" files to ".h" files.
>>June 2 - 9, 1999 - new distribution
(no version change)
Added additional DNA lambda/K/H to alt_param.h. Corrected some
other problems with those table. for the case where (inf,inf)
gap penalties were not included.
Fixed complib.c/comp_thr.c error message to properly report filename
when library file is not found.
Included approximate Lambda/K/H for BL80 in alt_parms.h.
BL80 scoring matrix changed from 1/3 bit to 1/2 bit units.
Included some additional perl files for searchfa.cgi, searchnn.cgi
in the distribution (my-cgi.pl, cgi-lib.pl).
>>May 30, 1999, June 2, 1999 - new distribution
(no version number change)
Added Makefile.NetBSD, if !defined(__NetBSD__) for values.h. Changed
zs_to_E() and z_to_E() in scaleswn.c to correctly calculate E() value
when only one sequence is compared and -z 3 is used.
>>May 27, 1999
(no version number change)
Corrected bug in alignment numbering on the % identity line
27.4% identity in 234 aa (101-234:110-243)
for reverse complements with offset coordinates (test.aa:101-250)
>>May 23, 1999
(no version number change)
Correction to Makefile.linux (tgetaa.o : failed to -DTFAST).
>>May 19, 1999
(no version number change)
Minor changes to pvm_showalign.c to allow #define FIRSTNODE 1.
Changes to showsum.c to change off-end reporting. (Neither of these
changes is likely to affect anyone outside my research group.)
>>May 12, 1999
--> v32t05
Fixed a serious bug in the fastx3/tfastx3 alignment display which
caused t/fastx3 to produce incorrect alignments (and incorrectly low
percent identities). The scores were correct, but the alignment
percent identities were too low and the alignments were wrong.
Numbering errors were also corrected in fastx3/tfastx3 and
fasty3/tfasty3 and when partial query sequences were used.
>>May 7, 1999
Fixed a subtle bug in dropgsw.c that caused do_work() to calculate
incorrect Smith-Waterman scores after do_walign() had been called.
This affected only pvcompsw searches with the "-m 9" option.
>>May 5, 1999
Modified showalign.c to provide improved alignment information that
includes explicitly the boundaries of the alignment. Default
alignments now say:
Smith-Waterman score: 175; 24.645% identity in 211 aa overlap (5:207-7:207)
>>May 3, 1999
Modified nxgetaa.c, showsum.c, showbest.c, manshowun.c to allow a
"not" superfamily annotation for the query sequence only. The
goal is to be able to specify that certain superfamily numbers be
ignored in some of the search summaries. Thus, a description line
of the form:
>GT8.7 | 40001 ! 90043 | transl. of pa875.con, 19 to 675
says that GT8.7 belongs to superfamily 40001, but any library
sequences with superfamily number 90043 should be ignored in any
listing or summary of best scores.
In addition, it is now possible to make a fasta3r/prcompfa, which is
the converse of fasta3u/pucompfa. fasta3u reports the highest scoring
unrelated sequences in a search using the superfamily annotation.
fasta3r shows only the scores of related sequences. This might be
used in combination with the -F e_val option to show the scores
obtained by the most distantly related members of a family.
>>April 25, 1999
-->v32t04 (not distributed)
Modified nxgetaa.c to remove the dependence of tgetaa.o on TFASTA
(necessary for a more rational Makefile structure). No code changes.
>>April 19, 1999
Fixed a bug in showalign.c that displayed incorrect alignment coordinates.
(no version number change).
>>April 17, 1999
--> v32t03
A serious bug in DNA alignments when the sequence has been broken into
multiple segments that was introduced in version fasta32 has been
fixed. In addition, several minor problems with -z 3 statistics on
DNA sequences were fixed.
Added -m 9 option, which unfortunately does different things in
pvcompfa/sw and fasta3/ssearch3. In both programs, -m 9 provides the
id's of the two sequences, length, E(), %_ident, and start and end of
the alignment in both sequences. pvcompfa/sw provides this
information with the list of high scoring sequences. fasta3/ssearch3
provides the information in lieu of an alignment.
>>March 18, 1999
--> v32t02
Added information on the algorithm/parameter description line to
report the range of the pam matrices. Useful for matrices like
MD_10, _20, and _40 which require much higher gap penalties.
>>March 13, 1999 (not distributed)
--> v32t01
-r results.file has been changed to -R results.file to accomodate
DNA match/mismatch penalties of the form: -r "+1/-3".
>>February 10, 1999
Modify functions in scalesw*.c to prevent underflow after exp() on
Alpha Linux machines. The Alpha/LINUX gcc compiler is buggy and
doesn't behave properly with "denormalized" numbers, so "gcc -g -m
ieee" is recommended.
Add "Display alignments also (y/n)[n] "
pvcomplib.c again provides alignments!! In addition, there is a
new "-m 9" option, which reports alignments as:
>>>/home/wrp/slib/hlibs/hum0.aa#5>HS5 gi:1280326 T-cell receptor beta chain 30 aa, 30 aa vs /home/wrp/slib/hlibs/hum0.seg library
HS5 30 HS5 30 1.873e-11 1.000 30 1 30 1 30
HS5 30 HS2249 40 1.061e-07 0.774 31 1 30 7 37
HS5 30 HS2221 38 1.207e-07 0.833 30 1 30 7 35
HS5 30 HS2283 40 1.455e-07 0.774 31 1 30 7 37
HS5 30 HS2239 38 1.939e-07 0.800 30 1 30 7 35
where the columns are:
query-name q-len lib-name lib-len E() %id align-len q-start q-end l-start l-end
>>February 9, 1999
Corrected bug in showalign.c that offset reverse complement alignments
by one.
>>Febrary 2, 1999
Changed the formatting slightly in showbest.c to have columns line up better.
>>January 11, 1999
Corrected some bugs introduced into fastf3(_t) in the previous version.
>>December 28, 1998
Corrected various problems in dropfz.c affecting alignment scores
and coordinates.
Introduced a new program, fasts3(_t), for searching with peptide
sequences.
>>November 11, 1998
--> v32t0
Added code to correct problems with coordinate number in long library
sequences with tfastx/tfasty. With this release, sequences should be
numbered properly, and sequence numbers count down with reverse
complement library sequences.
In addition, with this release, fastx/y and tfastx/y translated
protein alignments are numbered as nucleotides (increasing by 3,
labels every 30 nucleotides) rather than codons.
./fasta-36.3.8h/doc/readme.v33t0 0000644 0001054 0001054 00000142775 13525131122 013477 0 ustar wrp
$Id: readme.v33t0 342 2010-06-28 19:57:56Z wrp $
$Revision: $
================ readme.v33t0 ================
This release includes an MPI implementation of the parallel
library-vs-library comparison code. See readme.mpi_3.3 and
readme.pvm_3.3 for more information.
=====
>>July 9, 2001
Considerable changes to support no-global library functions.
(1) Separate ascii/sequence mapping arrays are used by the
query-reading (qascii), library-reading (lascii), and sequence
comparison function (pascii) routines. As a result, there is no
longer a need for tgetlib.o/lgetlib.o - lgetlib.o can serve both
functions.
(2) This also allows us to remove all #ifdef TFAST/FASTX conditionals
from complib.c/comp_thr.c/p2_complib.c. We no longer need
tcomp_thr.o, comp_thrx.o, etc. We still have a variety of
p2_complib.o variations to support the different c34.work* files.
(3) Because non-global openlib/getlib functions are available, exactly
the same open/get functions are available for reading both the
query and reference libraries in pv34comp* programs. The
host-specific openlib/getlib functions in hxgetaa.c are now
provided by nmgetlib.c, etc. This has two effect:
(a) it is now possible to compare a query database generated by an
SQL query to a library database generated by a different SQL
query.
(b) pv34comp* has lost (at least in this version) the ability to
automatically detect the query sequence type. To search with a
DNA query, you MUST use "-n".
(4) the resetp() function is now responsible for almost all of the
function sepcific (TFAST/FASTX/etc) initializations. All of the
function specific code has been removed from complib.c/comp_thr.c
and most of it has been moved to initfa.c/resetp().
(5) manageacc.c has been merged into compacc.c (mostly prhist()).
(6) Although it may reflect a subtle bug in my code, it is not
possible to reliably run threaded/memory mapped versions of the
fasta34_t code. I have spent considerable time tracking down the
problem, and have determined that, in threaded code, something
happens during the thread initialization to corrupt the
description offset information used when files are memory mapped.
This never occurs when the unthreaded versions of the code are
used. And it does not occur under MacOSX, Compaq Tru64Unix, Sun
Solaris/Sparc, or SGI IRIX.
Thus, I cannot recommend using the threaded code versions (_t)
under Linux (RH6.2 or 7.1).
=====
>>June 1, 2001
Many changes to accomodate a new - no global variable - strategy for
reading sequence databases. Every time a file is opened, a struct
lmf_str is allocated which can be used for memory mapped files, ncbl2,
files, and mysql files.
In addition, an open'ed file has a default sequence type: DNA or
protein, or one can open a file in a mode that will allow the sequence
type to be changed.
=====
>>May 18, 2001 CVS: fa33t09d0
A new compile time parameter - -DGAP_OPEN, is available to change the
definition of the "-f gap-open" parameter from the penalty for the
first residue in a gap to a true gap-open penalty, as is used in BLAST
and many other comparison algorithms. This will probably become the
default for fasta in version 3.4.
Fixes to conflicts between "-S" and "-s matrix". When a scoring
matrix file was specified, lower-case alignments were not displayed
with -S (although the scores were calculated properly).
More extensive testting of mysql_lib.c (mySQL query-libraries) with
the pv4comp* and mp4comp* programs.
=====
>>April 5, 2001 CVS: fa33t08d4b3
Changes in nmgetlib.c and ncbl2_mlib.c to return long sequence
descriptions for PCOMPLIB (pv4/mp3comp*). Also fix p2_complib.c to
request DNA library for translated comparisons.
Fix for prss33(_t) to read both sequences from stdin.
=====
>>March 27, 2001 CVS: fa33t08d4
--> fa33t08d4
Problems in ncbl2_mlib.c found searching NCBI non-redundant nucleotide
database "nt" were fixed. Testing revealed a minor memory leak, which
was fixed by modifying showbest.c, showalign.c, comp_thr.c, complib.c,
and p2_complib.c to remember the last opened database file more
effectively.
Modifications to allow 64-bit fseek/ftell on machines like Sun,
Linux/Intel, that support -D_FILE_OFFSET_BITS=64, -D_LARGE_FILE_SOURCE
off_t, and fseeko(), ftello() with the option -DUSE_FSEEKO. Machines
with 64-bit long's do not need this option. Machines with 32-bit
longs that allow files >2 Gb can do so with 64-bit file access
functions, including fseeko() and ftello(), which work with off_t file
offsets instead of long's.
=====
>>March 3, 2001 CVS: fa33t08d2
Corrected problems in nmgetaa.c and mysql_lib.c with parallel
programs, and one serious problem with alternate DNA scoring matrices
(initfa.c, initsw.c) not being set properly. A subtle problem with
the merge of scaleswn.c and scaleswg.c is fixed.
>>February 17, 2001
Modified mysql_lib.c to use "#", rather than "%ld", to indicate the
position of the GID. This change was made because sprintf() cannot be
used reliably to generate an SQL string, as '"' and '%' are used in
such strings.
=====
>>January 17, 2001
(no version change, date change)
Minro fixes to initfa.c, initsw.c to deal with DNA scoring matrices
properly. "-n -s dna.mat" is required for the sequence/matrix to be
recognized as DNA.
>>January 16, 2001
-->v34t00
Merge of the main CVS trunk - fa33t06 with the latest release branch,
fa33t08.
In addition, PCOMPLIB mods have been made to mysql_lib.c. Because
p2_complib.c gets sequence description information during the first
read of the database, the mysql_query must be changed to return:
result[0]=GID, result[1]=description, result[2]=sequence. In the
PCOMPLIB case, the other SQL queries (for GID description, sequence)
are not necessary but must still be provided.
=====
>>January 16, 2001
(no version change, previous version not released)
changes to p2_complib.c to correct openlib() incompatibility.
changes to nmgetaa.c, ncbl2_lib.c to incorporate PCOMPLIB. nxgetaa.c
removed.
=====
>>January 12, 2001
(no version change, previous version not released)
Change to initfa.c to move ktup check from query_parm() to last_init().
=====
>>January 10, 2001
--> v33t08
Fixes to complib.c, comp_thr.c to deal properly with long query
protein sequences when a short library chunk (e.g. -N 5000) was given.
In the case where the chunk size is too short, it will be reset to a
length which allows the search to proceed, by including an amount of
new sequence that is equal to the amount of overlap sequence.
scaleswn.c and scaleswg.c have been merged.
v33t08 includes the initial implementation for mySQL described below
for v33t07x.
======
>>Dec. 20, 2000
--> v33t07x
Initial implementation of a syntax for mySQL database queries. A new
file, mysql_lib.c has been added, and changes have been made to
nmgetaa.c (which should now replace nxgetaa.c) and altlib.h. A mySQL
database search needs a file with 4 parts:
(1) description of the database, user, password
(2) a select statement that generates the set of protein sequences
as: UID, sequence
(3) a select statement that generates a UID, description given a UID
(4) a select statement that generats a single UID, sequence given a UID
Each of the four parts should be separated by ';'. For example, in
the database that we are using for testing, a file "demo.sql" that
contains:
================
localhost taxonomy username secret;
SELECT proteins.gid, proteins.sequence FROM proteins,swissprot WHERE proteins.gid=swissprot.gid AND swissprot.spid IS NOT NULL;
select proteins.gid, concat(swissprot.spid," ",proteins.description) from proteins,swissprot where proteins.gid=%ld AND swissprot.gid=proteins.gid;
select gid, sequence from proteins where gid=%ld;
================
will find all the proteins in the BLAST "nr" database that also have
SwissProt ID's when given the command line:
fasta33 -q query.aa "demo.sql 16"
At least for simple queries, there is surprisingly little overhead for the
search. For more complex queries involving several tables, the overhead
can be significant.
At the moment, libraries that need the functions in mysql_lib.c will
use library type 16. We may also use file type 17 for SQL queries
that return binary sequences.
This implementation of mysql_lib.c was written to require a minimal
amount of change to the other programs. Only nmgetaa.c and altlib.h
needed to be changed to incorporate this new capability. One result
of this limitation is that one cannot mix mySQL databases queries with
other databases in the same search. Eventually, I would like to make
a mySQL database like any other, so that several mysql database
queries could be searched in the same run, and mysql databases could
be mixed with other (flat file) databases, but this will require some
changes in the function calls throughout the code. (Right now, the
various programs do not distinguish between an openlib() that is made
before searching a large database, and one before retrieving a single
sequence. This must be changed for a database query like mySQL to
behave like other databases.
Several mySQL demo files have been provided: mysql_demo*.sql.
(10 January 2001) The mySQL code has been tested on Intel Linux and
Compaq/Alpha/Tru64 Unix.
>>Dec. 9, 2000
Changes to apam.c that to tie different default gap penalties to
alternate scoring matrices. In addition, changes to apam.c, to deal
with user-specified matrices with or without '*'.
>>Nov. 5, 2000 (date updated)
pst.dnaseq can now have 3 values, -1, or 0-> protein, 1->DNA, and 2->other.
This becomes important for thing like init_karlin_a, which needs a
background frequency of residues.
>>Nov. 1, 2000
Significant bug fixes for the -z 6/-z 16 option. An ininitialized
variable was fixed in karlin.c, and comp_thr.c did not pass the
correct composition argument type in find_zp(). The -z 6/16 option
has now been tested and works correctly on Alphas, Linux x86, SGI, Sun
and Mac OSX. Another problem was fixed in scaleswn.c (simplex()) that
prevented the code from being reused by the pv4/mp4 complib programs.
>>Oct. 9, 2000
Several changes made to accomodate Mac OSX. Longer lists of superfamily
numbers now supported in p[su]4comp/m[su]4comp programs.
>>Sept 25, 2000
All global variables have been removed from scaleswn.c. The last to
go, db_struct db, required many edits, because until now, the fasta
programs have kept two versions of the db_struct data (entries,
length). One version was kept by the main program, which updated entry
number and db length as sequences were read; a second copy of this
information was kept by the statistical estimation routines. Now
there is only one copy, which means that the E() values will be a
function of the complete database, not the database with some high
scoring sequences removed.
>>Sept 23, 2000
Continued removal of global variables from scaleswn.c. Only one
global is left, db_struct db, which contains the number of entries in
the database and the number of residues. It will be the next to go
(changing all the zs_to_*() functions) and scaleswn. will be free
of globals. scaleswg.c is gone - scaleswn.c compiles to scaleswg.c
with -DNORMAL_DIST.
>>Sept 20, 2000
Removal of histogram globals required changes in p2_complib.c as well.
p_complib.c has not been updated. scaleswg.c has been modified to
reflect the new histogram strategy.
>>Sept 19, 2000
Substantial changes to remove globals for printing histogram. m_msg
now contains a hist_str, which keeps histogram information.
>>Sept. 19, 2000
(no version change, previous version not released)
Correct bug introduced into scaleswn.c (inithist()) by changing
score2_sums[], score_sums[] from int to double.
Reporting of version numbers is more consistent between fasta33,
fasta33_t, and pv4compfa/mp4compfa. The programs now report the same
numbers/dates in similar places.
>>Sept. 15, 2000
--> v33t07
Changes to fix problems with statistical estimates when a large
fraction (but not all) of the database is related. Several users
reported problems when searching with rRNA genes with version 33t06.
In some cases, a 100% identitical match over 1500 nt would not be
statistically significant against a search of the bacterial division
of Genbank. This problem was not seen with some releases of v33t05.
The cause of the problem was a change between v33t05 and v33t06 to
allow scoring matrices with unusual scaling to be used. In v33t05,
there was a line that excluded all scores > 300 from the statistical
estimation procedure. While 300 is a high score with any "normal"
scoring matrix, some investigators were using matrices scaled 10X, so
that a score of 300 was really a score of 30 with a conventional
matrix, and should not be excluded. Unfortunately, removing the test
to exclude scores > 300 meant that when a rRNA sequence was used to
search the bacterial division, tens of thousands of high scoring
related sequences were treated as if they were unrelated, with the
result that the variance estimates were much too high, and thus high
real scores had low z-scores, and thus were not statistically
significant. (There appear to be more than 20,000 rRNA sequences in
the bacterial division of Genbank, almost 25% of all sequences).
The solution to the problem is a substantial enhancement in the
strategies used to exclude high-scoring, related sequences, the -z 1,
4, and 5 parameter estimation strategies. The programs now estimate
the expected high scoring sequence by calculating an ungapped Lambda
and K, and then use a relatively conservative threshold for excluding
scores that are higher than would be expected 0.01 times by chance.
By calculating Lambda and K, we can scale the cutoff thresholds to
allow scoring matrices with unusual scales. For "normal" searches,
there should be little change, but there should be an improvement for
searches with large numbers of related sequences in the database.
As a result of testing for this change, a bug in the karlin() function
used with -z 6 was found and corrected.
=======
>>Sept. 9, 2000
Changes to manshowbest.c to include correct display coordinates.
Significant changes to structs.h, param.h, p2_complib.c,
p2_workcomp.c, to store and use a reliable a_struct for alignment
coordinates.
Other cosmetic changes.
>>Sept. 7, 2000
Minor changes to complib.c, showrss.c, so that prss33 -q uses 200
shuffles and prss33 provides bit scores, rather than z-scores.
(no version number change).
Modifications to p2_complib.c to include superfamily numbers for
ps4comp* ms4comp*.
>>Aug 22, 2000
Changes to mmgetaa.c, ncbl2_mlib.c, dropfs.c to accomodate AIX.
00README.1st updated to reflect the current version and correct
outdated information on threads.
>>Aug. 3, 2000
Modifications to initpam2() in initsw.c to correct a problem with pam_x
when the -S option is used.
Modifications to compacc.c, scaleswn.c to ensure that residue numbers
are calculated properly when more than 2 Gb of sequence is searched.
>>July 12, 2000
Modifications to dropnfa.c so that DNA matches to 'N' will be included
in the "ungapped %identity". Thus, a sequence that is 100% identical
for 100 nt on either side of a 100 nt region that has been masked to
'NNNNN' will be reported as: "67% identical (100% ungapped)". This
has been added to deal with masked BAC-end databases. It would be
better if masking changed the letters to lowercase, but the mouse
BAC-end sequences at TIGR use 'NNNNN'. This is currently available
only for the fasta function, not [t]fast[x/y], etc, and only for DNA
sequences.
mk_n_pam() in apam.c modified to ensure that mismatch scores of -1
remain -1.
>>June 25, 2000
Modification to nxgetaa.c, nmgetaa.c, mmgetaa.c to return Genbank Accession
number as part of the descriptive string.
>>June 11, 2000
(no version change - not yet released)
Modifications to calcons(), calc_id(), showbest(), p_workcomp.c to
provide ngap_q (number of alignment gaps in query) , ngap_l (number
of gaps in library) information for -m 9 output.
>>June 6, 2000
(no version change - not yet released)
Modified scaleswn.c to provide better support for unconventional
scoring scoring matrices, in particular, scoring matrices where every
value is 50-times higher. Previous versions of the MLE estimator (-z
2) started with lambda = 0.2, which is too high for a scoring matrix
going from -500:+1500. The initial estimate for lambda is now
calculated using the formula: lambda = pi/sqrt(6*variance). For the
default -z 1, a restriction to limit scores to a maximum of 300 for
the statistical analysis was removed.
>>June 3, 2000
Modified aligment output, and -m 9 and -m10, to report an "ungapped"
identity as well as the traditional "gapped" identity. The
traditional "gapped" identity reports the number of identities divided
by the overall length of the alignment, including gaps. The
"ungapped" identity does not include gaps in the length of the
alignment. This new value is included for alignments that include
introns; thus, a tfastx33 search might find the 100% identical genomic
sequence but report the gapped percent identity if a short intron were
included in the alignment (the alignment probably would not span a
long exon) as 66%. The "ungapped" identity would remain 100%. The
ungapped identity value is also shown in the "-m 9" output line after
the "gapped" fraction identical.
>>June 1, 2000
Modified -m 9 output to provide fraction identical, alignment boundary
information with the initial list of high scoring sequences, just as
the pv3comp and mp_comp versions do. The -m 9 option now shows the
same alignment display as -m 0, but the width of the alignment is
increased by 40. Thus, by default, -m 9 will show the list of best
hits, with percent identity, Smith-Waterman score, and alignment
boundaries initially, and then show alignments standard (-m 0)
alignments with 100 residues/line.
>>May 29, 2000
Correct some problems with reading data files with 's under unix.
nmgetaa.c/nxgetaa.c/mmgetaa.c have been modified to convert
('\t') to (' ') in descriptive lines.
=======
>>May 3, 2000
Corrected problem with very low mean_var in fit_llen() in scaleswn.c.
>>May 2, 2000
(no version number change - previous version not released)
Merged fasta33t05d2 with fasta33t06. Also removed restriction on
"-M size-range" to proteins - the size range now can be applied to DNA
as well.
>>May 1, 2000
(changes to v33t05d merged into v33t06)
Introduced changes to include '*' as a valid sequence character, which
indicates termination. Thus, 'TGA', 'TAG', and 'TAA' are now
tranlated to '*' rather than 'X', and the protein PAM matrices have
been modified to provide a match score of approximately 1/2 the max
identity score for a '*:*' match. Otherise, '*' is the same as 'X'.
This change only affects query sequences that include a '*' to
indicate an end of sequence, the '*' is not there by default.
The inclusion of '*' broke some things in tfasts33, tfastf33, fasty33,
and tfasty33, which were fixed today.
>>March 28, 2000/April 24, 2000
--> v33t06
(a) -z 6 statistics that factor in composition
(b) -smatrix-offset pam-offset parameter
(a) This release provides a new statistics option, -z 6, which
provides a more sophisticated model that accounts for sequence
composition. When -z 6 is used (only for fasta33(_t) and
ssearch33(_t)), the program calculates a composition parameter
comp=1/lambda using a modified version of the Karlin-Altschul karlin()
function. As a result, every sequence in the database has an
associated length (n1) and composition (comp).
The length n1 and composition comp are used in the maximum likelihood
estimation described by Mott (1992) Bull. Math. Biol. 54:59-75. Four
parameters are estimated, a0, a1, a2, and b1, and the probability of
obtaining a score is then:
p(s >= x) = 1-exp(-exp(-( a0 + a1*comp + a2*comp*log(n0*n1) + x)/(b1*comp)))
The maximum likelihood estimates of a0, a1, a2, and b1 are calculated
using the Nelder-Mead simplex search strategy.
The average Lambda is reported for the search using Lambda =
1/(b1*ave_comp). Where ave_comp is the geometric mean of the comp values
calculated during the statistical estimates.
The "lambda/comp" calculation can fail for sequences with very biased
amino acid composition. When this occurs, 'comp' is set to -1.0 (as
is 'H', the information content parameter) and the 'ave_comp' value is
used to calculate statistical significance. (But obviously 'ave_comp'
is not really appropriate, since if the sequence had an average 'comp'
value, it would have been calculated.) When -z 6 is used, the
alignment display shows the 'comp' and 'H' values for that library
sequence.
(b) Scoring matrix offsets - The main reason that the "lamdba/comp"
calculation fails is that, for the particular query/library sequence
pair, the expected score is not < 0, instead, Sum {p_ij S_ij} >= 0.0.
This problem is reported to 'stderr' when it occurs. The simplest
solution to the problem is to provide an offset to the scoring matrix;
for example, to use Blosum62 - 1, which ranges from +10 to -5, rather
than the standard +11 to -4. This option used to be available with
the -S offset option, but -S is now used to specify a lower-case
seg-ed database. The offset can now be specified as part of the
scoring matrix name. Thus, "-s BL62-1" uses Blosum62 reduced by 1 at
each entry. The '-' character is used to indicate an offset, so
scoring matrix files must not have a '-' in their name.
Alternatively, "-s BL80+1" or "-s BL80--1" would add one to each value.
nxgetaa.c, nmgetaa.c, and mmgetaa.c have been edited to avoid string
run-off problems after strncpy().
Fixed problem where positive gap extension penalties in ssearch33
were not converted to negative values.
>>April 8, 2000
Fixed problem in calculating corrected sequence lengths for
Altschul-Gish probabilities.
>>March 30, 2000
(no version change, date updated to March 30, 2000)
Corrected problem with -m 9 option.
The '*' character is now available to allow translated alignments to
extend through the termination codon. Thus, if a protein sequence ends
with a '*', and matches in to a translated termination codon, the
score will be increased. The *:* match score is set to 1/2 the max
positive score for the matrix (see upam.h). This strategy can also be
used to upweight a match that extends all the way to the end of a
full-length sequence by putting '*' at the end of both the query and
library protein sequences. Recognition of '*' will probably become a
command line option.
>>March 21, 2000
(no version change, previous version not distributed)
Changes to map_db.c, list_db.c, and mmgetaa.c to accomodate large
sequence files. Long (64-bit on some systems) variables are now used
to specify file and memory position for the memory mapped functions.
As a result, there are now two *.xin (memory mapped index) file
formats: MP0, which uses 32-bit longs, and MP1, which uses 64-bit
longs. On 64-bit machines, MP0 32-bit indices are read properly, but
limit the database size to 2 or 4 Gb; MP1 64-bit indices allow very
large databases. Blast2.0 formatdb databases are still limited to
4Gb. To compile map_db.c to generate 64-bit index files, include the
compile time option -DBIG_LIB64 in the Makefile. (Currently this
option has been tested only on the DEC Alpha and SGI platforms, and
will work only with Unix versions that provide 64-bit longs and 64-bit
ftell()'s.)
The -R results file now uses sfn_cmp() to report a matching
superfamily number, if one exists, and '0' otherwise.
>>March 12, 2000
(no version change, previous version not distributed)
Provide new strategy for specifying library abbreviations. In
addition to:
fasta33 query.aa %anr
one can also specify:
fasta33 query.aa %pir1+sp+nr
or
fasta33 query.aa +pir1+sp+nr
or
fasta33 query.aa %+pir1+sp+nr
where the + anywhere in the library name string indicates that
variable length library names, separated by '+', are being used (the
last '+' is optional). The FASTLIBS file then becomes:
================
PIR1 Annotated Protein Database (rel 56)$0+pir1+/slib2/blast/pir1.lseg
NBRF Protein database (complete)$0+nbrf+@/seqlib/lib/NBRF.nam
NRL_3d structure database$0D/seqlib/lib/nrl_3d.seq 5
NCBI/Blast non-redundant proteins$0+nr+/slib2/blast/nr.lseg
NCBI/Blast Swissprot$0+sp+/slib2/blast/swissprot.lseg
================
The two abbreviation types, single letter and +word+, cannot be
intermixed, and at least initially, +word+ specifiers are
case-sensitive (single letter abbreviations are not) and will not be
available interactively, only on the command line.
Removed 'K' estimate for Expectation_n, Expectation_i fits to the
distribution of unrelated similarity scores. 'K' cannot be calculated
from the data available. 'Lamdba' can be calculated, it is
1.28255/sqrt(mean_var), and is still available.
>>March 3, 2000
(no version change)
changed Makefile33.common, Makefile.common, to incorporate $(NRAND)
rather than "rand48". Provide nrandom.c which uses random(), as
replacement for nrand.c, which uses rand48().
>>February 8, 2000
--> v33t05
Fixes to scaleswn.c (proc_hist_ml) to set num_db_entries properly.
Scaleswn.c also provides Lambda estimates for -z 1/11 (Expectation_n),
and -z 1/14 (Expectation_i) statistical estimates.
Modifications to calc_id() to correct bug in counting identities.
Modified showalign() to use calc_id() with -m 9, for simpler
debugging.
Additional modifications to dropfa*.c files to deal properly with 'n's
and 'x's.
Added new option: -x #, which allows one to override the penalty for a
match against 'x' (or 'N') provided by the scoring matrix. This
option is particularly useful in fast[x/y] searches, where out of
frame low complexity regions can generate high scores.
The old function of '-x' - to specify an alternate coordinate system,
is now available as '-X # #'.
Updated scaleswn.c to provide window shuffle information for -z 12.
Updated compacc.c, workacc.c, to fix serious bug in wshuffle()
that destroyed aa1[n1]=0.
>>January 25, 2000
--> v33t04
A serious bug in all of the fasta related programs has been
corrected. The new code in fasta33 which ignores certain residues
failed to initialize one of the arrays properly. As a result, in
pathological situations, a very strong match could be missed.
Corrected minor bug in initsw.c that cause misplaced "ktup" command
line argument, which should be ingnored by ssearch, to be read as -d
ktup.
Improved error message for 0 length query sequence.
>>January 17, 2000
--> no external version number change
Modified mmgetaa.c, map_db.c, and nmgetaa.c to provide memory mapping
of genbank flatfile (format=1) files. This format could be read much
more efficiently, however.
>>January 12, 2000
--> no external version number change
Changed the behavior of the options that set the number of high scores
(-b) and alignments (-d) that are displayed. Previously, fasta33 -E
10.0 -d 10 would show 50 best scores, rather than all the scores with
E() < 10.0. To get the -E threshold to limit, -E 10.0 -b 10000 -d 10
was required. This is now fixed. Setting "-d 10" does not affect the
number of best scores shown.
Minor change in mw.h to remove unused defines.
fasta3x.me (fasta3x.doc) updated.
>>January 6, 2000
--> v33t03
Corrected bug in memory mapped reads of gcg_binary format files
that potentially caused the last 63 residues to be read improperly.
Changes to comp_thr.c, pthr_subs.c, uthr_subs.c, ibm_pthr_subs.c to
ensure that each thread has its own work_info structure. This solves
some minor race conditions that sometimes caused some parameters
not to be reported properly.
Changes to most of the drop*.c files to correct some minor problems
with sequence alphabets. Code in mmgetaa.c (memory mapped code for
FASTA, GCG compressed files) reordered to prevent files from being
memory mapped if appropriate index files are not available.
See readme.pvm_3.3 for updates to the pvm programs.
>>December 10, 1999
(no version change - modifications largely affect ps3comp*)
Modifications to showsum.c to deal with 2 scores/sequence. Modifications
to mmgetaa.c for superfamily numbers.
>>December 7, 1999
(no version change, previous version not released)
Corrected problem in mmgetaa.c that caused searches on a memory mapped
single long sequence (e.g. Chr22) to fail. Corrected bug in map_db.c
that caused it to crash on some architectures if a filename was not
specified. Corrected off-by-three error in fasty/tfasty. Corrected
indexing error in dropfz2.c.
>>December 5, 1999
--> v33t02
corrected some bugs in inifa.c/initsw.c/doinit.c that caused
abbreviated function names to be lost.
modify showbest.c, showalign.c to include information on position in
library sequence (bbp->cont) to distinguish subsegment of very long
sequences. Currently, the new label is available only with -m 6.
>>November 29, 1999
[t]fastz33 uses v33t02 of fasty function.
Replace dropfz.c with dropfz2.c. Dropfz2.c interprets any codons,
that include the nucleotide 'N' as the amino 'X'. Previously, 'N' was
treated as 'A', so 'NNN' ended up 'K'. This modification, together
with the -S option and lower-case pseg'ed databases, should ensure
that DNA queries with large numbers of 'N's do not match low
complexity regions.
>>November 20, 1999
(no version change, previous version not released)
Modify initfa.c to disply initn, init1 scores for [t]fast[fs].
Include "-B" option to show previous z-scores.
>>November 17, 1999
(no version change, previous version not released)
Modify dropfx.c to use saatran(), rather than aatran(). saatran
translates any 'N' containing codon as 'X'. aatran() treats 'N' as
an 'A'. Although more steps are required for translation, the program
appears to run just as fast.
>>November 7, 1999
--> v33t01
Substantial changes to the output format in showbest.c (the list of
high scoring sequences) and showalign.c (the alignments). The classic
list of best scores:
The best scores are: initn init1 opt z-sc E(82014)
gi|121716|sp|P10649|GTM1_MOUSE GLUTATHIO ( 218) 1497 1497 1497 1761.1 2.3e-91
gi|121717|sp|P04905|GTM1_RAT GLUTATHIONE ( 218) 1413 1413 1413 1662.9 6.7e-86
has been replaced by:
The best scores are: opt bits E(82138)
gi|121716|sp|P10649|GTM1_MOUSE GLUTATHIONE S-TRAN ( 218) 1497 354 7.6e-98
gi|121717|sp|P04905|GTM1_RAT GLUTATHIONE S-TRANSF ( 218) 1413 335 5.3e-92
This display provides more information and removes the outdated initn
and init1 scores, which are no longer used. The "bit" score is
comparable to the blast2 bit score. It is calculated as: (lambda*S -
ln K)/ln 2, where S is the raw similarity score, lambda and K are
statistical parameters estimated from the distribution of unrelated
sequence similarity scores. All of the similarity scores, including
init1, initn, and z-scores are reported with the alignment data.
Z-scores are displayed instead of bit scores in the list of high
scores if the command line option "-B" is specified.
In addition, the alignment score line has changed from:
>>gi|2506495|sp|P20136|GTM2_CHICK GLUTATHIONE S-TRANSFER (220 aa)
initn: 954 init1: 954 opt: 958 Z-score: 1130.9 expect() 1.1e-56
Smith-Waterman score: 958; 61.927% identity in 218 aa overlap (1-218:1-218)
to:
>>gi|2506495|sp|P20136|GTM2_CHICK GLUTATHIONE S-TRANSFER (220 aa)
initn: 954 init1: 954 opt: 958 Z-score: 1130.9 bits: 216.4 E(): 2.8e-56
Smith-Waterman score: 958; 61.927% identity in 218 aa overlap (1-218:1-218)
In addition to the addition of the "bits:" score, the "expect()" label
has changed to "E()" to save some space.
>>November 4,12, 1999
(no version change)
Fixed serious bug in -z 2 lambda/K calculation in scaleswn.c
Fixed bugs in llgetaa.c (openlib()) and definition of superfamily
numbers.
>>October 21, 1999
(no version change)
Begin using CVS for version control. Correct faulty error message in
dropfs.c. Corrected bad "goto loopl;" in dropfz.c. Corrected prss3.rsp
for Makefile.tc (Win32 version).
>>October 18, 1999
--> v33t0
Corrected some serious bugs with the various fasta/x/y programs when
the -DALLOCN0 was used to save memory. Improvements to fasta3x.me/.doc
documentation.
>>October 12, 1999
--> v33tx
For this initial release of version 33 of the FASTA programs, the
Makefile's have been modified to make "fasta33(_t)", "fastx33(_t)",
etc, so that you can test fasta33 while retaining fasta3 (from release
v32t08). The FASTA33 programs are somewhat slower than previous
releases, but I believe the ability to handle low complexity regions
without 'X'ing them out outweighs the slowdown. By (temporarily)
changing the names of the programs slightly, it will be easier for you
to judge the relative cost and benefit. To "make" the programs as
"fasta3(_t)", etc, simply replace "Makefile33.common" with
"Makefile.common" in the "Makefile" that you use.
>>September 30, 1999
ssearch3/fasta3/fastx3/fasty3 have been modified to search databases
containing both upper and lower case letters, where lower case letters
indicate low-complexity regions. With the modified programs, lower
case letters are treated as 'X's' in the initial scan, but are then
treated normally in the final alignment. In addition, alignments can
contain lower case letters. Lower case letters are treated as
low-complexity regions during the seach phase of the program, but as
"conventional" residues during the alignment phase, with the "-S"
option. Currently, lower case letters are mapped to 'X's during the
scan of the entire library. In the future, alternate weights will be
available. This is a substantial improvement for very large scale
comparison, where one seeks both accurate statistical estimates and
accurate %identities and alignments, and for translated DNA:protein
comparisons, like "fastx3" and "fasty3", where out-of-frame
translations tend to match low complexity regions (see Pearson et
al. (1997) Genomics 46:24-36).
Protein databases (and query sequences) can be generated in the
appropriate format using John Wooton's "pseg" program, available from
ftp://ftp.ncbi.nih.gov/pub/seg/pseg. Once you have compiled the "pseg"
program, use the command:
pseg database.fasta -z 1 -q > database.lc_seg
Once you have database.lc_seg, run the command "map_db" to generate
a ".xin" file that can be used to efficiently memory map the database.
You can then search database.lc_seg with or without the "-S" option.
Without "-S", the database is treated as any other FASTA format file -
all the residues are present. With "-S", lower case residues will be
treated as 'x's' during the initial scan but as normal residues when
final alignments are displayed.
When the -S option is used, the matrix information line is changed
from: "BL50 matrix (15:-5)" to "BL50 matrix (15:-5)xS". The "-S"
option is no longer available to provide a scoring matrix offset.
Unfortunately, Blast2.0 format files cannot contain lower case
letters. We have addressed this problem by providing efficient memory
mapped access to Fasta and GCG/PIR, and GCG/compressed-binary files in
the last release of fasta32t08. The memory mapped file I/O
improvements are provided in fasta33 as well.
================ readme.v32 ================
FASTX/Y and FASTA (DNA) are now half as fast, because the programs now
search both the forward and reverse strands by default.
The documentation in fasta3x.me/fasta3x.doc has been substantially
revised.
>>October 20, 1999
(no version change)
Modify nxgetaa.c/nmgetaa.c to recognize 'N' as a possible DNA character.
>>October 9, 1999
--> v32t08 (no version number change)
Added "-M low-high" option, where low and high are inclusion limits
for library sequences. If a library sequence is shorter than "low" or
longer than "high", it will not be considered in the search. Thus,
"-M 200-250" limits the database search to proteins between 200 and
250 residues in length. This should be particularly useful for fasts3
and fastf3. -M -500 searches library sequences < 500; -M 200 -
searches sequences > 200. This limit applies only to protein
sequences.
Modified scaleswn.c to fall back to maximum likelihood estimates of
lambda, K rather than mean/variance estimates. (This allows MLE
estimation to be used instead of proc_hist_n when a limited range of
scores is examined.)
>>October 2, 1999
--> v32t08
Many changes:
(1) memory mapped (mmap()ed) database reading - other database reading fixes
(2) BLAST2 databases supported
(3) true maximum likelihood estimates for Lambda, K
(4) Misc. minor fixes
(1) (Sept. 26 - Oct. 2, 1999) Memory mapped database access.
It is now possible to use mmap()ed access to FASTA format databases,
if the "map_db" program has been used to produce an ".xin" file. If
USE_MMAP is defined at compile time and a ".xin" file is present, the
".xin" will be used to access sequences directly after the file is
mmap()ed. On my 4-processor Alpha, this can reduce elapsed time by
50%. It is not quite as efficient as BLAST2 format, but it is close.
Currently, memory mapping is supported for type 0 (FASTA), 5
(PIR/GCG ascii), and 6 (GCG binary). Memory mapping is used if a
".xin" file is present. ".xin" files are created by the new program
"map_db". The syntax for "map_db" is:
map_db [-n] "/dir/database.fa"
which creates the file /dir/database.fa.xin. Library types can be
included in the filename; thus:
map_db -n "/gcggenbank/gb_om.seq 6"
would be used for a type 6 GCG binary file.
The ".xin" file must be updated each time the database file changes.
map_db writes the size of the database file into the ".xin" file, so
that if the database file changes, making the ".xin" offset
information invalid, the ".xin" file is not used. "list_db" is
provided to print out the offset information in the ".xin" file.
(Oct 2, 1999) The memory mapping routines have been changed to
allow several files to be memory mapped simultaneously. Indeed, once a
database has been memory mapped, it will not be unmap()ed until the
program finishes. This fixes a problem under Digital Unix, and should
make re-access to mmap()ed files (as when displaying high scores and
alignments) much more efficient. If no more memory is available for
mmap()ing, the file will be read using conventional fread/fgets.
(Oct 2, 1999) The names of the database reading functions has been
changed to allow both Blast1.4 and Blast2.0 databases to be read. In
addition, Makefile.common now includes an option to link both
ncbl_lib.o and ncbl2_lib.o, which provides support for both libraries.
However, Blast1.4 support has not been tested.
The Makefile structure has been improved. Each architecture specific
Makefile (Makefile.alpha, Makefile.linux, etc) now includes
Makefile.common. Thus, changes to the program structure should be
correct for all platforms. "map_db" and "list_db" are not made with
"make all".
The database reading functions in nxgetaa.c can now return a database
length of 0, which indicates that no residues were read. Previously,
0-length sequences returned a length of 1, which were ignored.
Complib.c and comp_thr.c have changed to accommodate this
modification. This change was made to ensure that each residue,
including the last, of each sequence is read.
Corrected bug in nxgetaa.c with FASTA format files with very long
(>512 char) definition lines.
(2) (September 20, 1999) BLAST2 format databases supported
This release supports NCBI Blast2.0 format databases, using either
conventional file reading or memory mapped files. The Blast2.0 format
can be read very efficiently, so there is only a modest improvement in
performance with memory mapping. The decision to use mmap()'ed files
is made at compile time, by defining USE_MMAP. My thanks to Eamonn
O'Toole of DEC/Compaq, and Daryl Madura of Sun Microsystems, for
providing mmap()'ed modifications to fasta3. On my machines, Blast2.0
format reduces search time by about 30%. At the moment, ambiguous DNA
sequences are not decoded properly.
(3) (September 30, 1999) A new statistical estimation option is
available. -z 2 has been changed from ln()-scaling, which never
should have been used, to scaling using Maximum Likelihood Estimates
(MLEs) of Lambda and K. The MLE estimation routines were written by
Aaron Mackey, based on a discussion of MLE estimates of Lambda and K
written by Sean Eddy. The MLE estimation examines the middle 95% of
scores, if there are fewer than 10000 sequences in the database;
otherwise it excludes (censors) the top 250 scores and the bottom 250
scores. This approach seems to effectively prevent related sequences
from contaminating the estimation process. As with -z 1, -z 12 causes
the program to generate a shuffled sequence score for each of the
library sequences; in this case, no censoring is done. If the
estimation process is reliable, Lambda and K should not vary much with
different queries or query lengths. Lambda appears not to vary much
with the comparison algorithm, although K does.
(4) Minor changes include fixes to some of the alignment display routines,
individual copies of the pstruct structure for each thread, and some
changes to ensure that every last residue in a library is available
for matching (sometime the last residue could be ignored). This
version has undergone extensive testing with high-throughput sequences
to confirm that long sequences are read properly. Problems with
fastf3/fasts3 alignment display have also been addressed.
>>August 26, 1999 (no version change - not released)
Corrected problem in "apam.c" that prevented scoring matrices from
being imported for [t]fasts3/[t]fastf3.
>>August 17, 1999
--> v32t07
Corrected problem with opt_cut initialization that only appeared
with pvcomp* programs.
Improved calculation of FASTA optcut threshold for DNA sequence
comparison for match scores much less than +5 (e.g. +3). The previous
optcut theshold was too high when the match penalty was < 4 and
ktup=6; it is now scaled more appropriately.
Optcut thresholds have also been raised slightly for
fastx/y3/tfastx/y3. This should improve performance with minimal
effects on sensitivity.
>>July 29, 1999
(no version change - date change)
Corrected various uninitialized variables and buffer overruns
detected.
>>July 26, 1999 - new distribution
(no version change - v32t06, previous version not released)
Changed the location of "(reverse complement)" label in tfasta/x/y/s/f
programs.
Statistical calculations for tfasta/x/y in unthreaded version
corrected. Statistical estimates for threaded and unthreaded versions
of the tfasta/x/y/s/f programs should be much more consistent.
Substantial modifications in alignment coordinate calculation/
presentation. Minor error in fastx/y/tfastx/y end of alignment
corrected. Major problems with tfasta alignment coordinates
corrected. tfasta and tfastx/y coordinates should now be consistent.
Corrected problem with -N 5000 in tfasta/x/y3(_t) searches encountered
with long query sequences.
Updated pthr_subs.c/Makefile.linux to increase the pthreads stacksize
to try to avoid "cannot allocate diagonal arrays" error message.
Pthreads stacksize can be changed with RedHat 6.0, but not RedHat 5.2,
so Makefile.linux uses -DLINUX5 for RedHat5.* (no pthreads stack size).
I am still getting this message, so it has not been completely
successful. Makefile.linux now uses -DALLOCN0 to avoid this problem,
at some cost in speed.
The pvcomp* programs have been updated to work properly with
forward/reverse DNA searches. See readme.pvm_3.2.
>>July 7, 1999 - not released
--> v32t06
Corrected bug in complib.c (fasta3, fastx3, etc) that caused core
dumps with "-o" option.
Corrected a subtle bug in fastx/y/tfastx/y alignment display.
>>June 30, 1999 - new distribution
(no version change)
Corrected doinit.c to allow DNA substitution matrices with -s matrix
option.
Changed ".gbl" files to ".h" files.
>>June 2 - 9, 1999 - new distribution
(no version change)
Added additional DNA lambda/K/H to alt_param.h. Corrected some
other problems with those table. for the case where (inf,inf)
gap penalties were not included.
Fixed complib.c/comp_thr.c error message to properly report filename
when library file is not found.
Included approximate Lambda/K/H for BL80 in alt_parms.h.
BL80 scoring matrix changed from 1/3 bit to 1/2 bit units.
Included some additional perl files for searchfa.cgi, searchnn.cgi
in the distribution (my-cgi.pl, cgi-lib.pl).
>>May 30, 1999, June 2, 1999 - new distribution
(no version number change)
Added Makefile.NetBSD, if !defined(__NetBSD__) for values.h. Changed
zs_to_E() and z_to_E() in scaleswn.c to correctly calculate E() value
when only one sequence is compared and -z 3 is used.
>>May 27, 1999
(no version number change)
Corrected bug in alignment numbering on the % identity line
27.4% identity in 234 aa (101-234:110-243)
for reverse complements with offset coordinates (test.aa:101-250)
>>May 23, 1999
(no version number change)
Correction to Makefile.linux (tgetaa.o : failed to -DTFAST).
>>May 19, 1999
(no version number change)
Minor changes to pvm_showalign.c to allow #define FIRSTNODE 1.
Changes to showsum.c to change off-end reporting. (Neither of these
changes is likely to affect anyone outside my research group.)
>>May 12, 1999
--> v32t05
Fixed a serious bug in the fastx3/tfastx3 alignment display which
caused t/fastx3 to produce incorrect alignments (and incorrectly low
percent identities). The scores were correct, but the alignment
percent identities were too low and the alignments were wrong.
Numbering errors were also corrected in fastx3/tfastx3 and
fasty3/tfasty3 and when partial query sequences were used.
>>May 7, 1999
Fixed a subtle bug in dropgsw.c that caused do_work() to calculate
incorrect Smith-Waterman scores after do_walign() had been called.
This affected only pvcompsw searches with the "-m 9" option.
>>May 5, 1999
Modified showalign.c to provide improved alignment information that
includes explicitly the boundaries of the alignment. Default
alignments now say:
Smith-Waterman score: 175; 24.645% identity in 211 aa overlap (5:207-7:207)
>>May 3, 1999
Modified nxgetaa.c, showsum.c, showbest.c, manshowun.c to allow a
"not" superfamily annotation for the query sequence only. The
goal is to be able to specify that certain superfamily numbers be
ignored in some of the search summaries. Thus, a description line
of the form:
>GT8.7 | 40001 ! 90043 | transl. of pa875.con, 19 to 675
says that GT8.7 belongs to superfamily 40001, but any library
sequences with superfamily number 90043 should be ignored in any
listing or summary of best scores.
In addition, it is now possible to make a fasta3r/prcompfa, which is
the converse of fasta3u/pucompfa. fasta3u reports the highest scoring
unrelated sequences in a search using the superfamily annotation.
fasta3r shows only the scores of related sequences. This might be
used in combination with the -F e_val option to show the scores
obtained by the most distantly related members of a family.
>>April 25, 1999
-->v32t04 (not distributed)
Modified nxgetaa.c to remove the dependence of tgetaa.o on TFASTA
(necessary for a more rational Makefile structure). No code changes.
>>April 19, 1999
Fixed a bug in showalign.c that displayed incorrect alignment coordinates.
(no version number change).
>>April 17, 1999
--> v32t03
A serious bug in DNA alignments when the sequence has been broken into
multiple segments that was introduced in version fasta32 has been
fixed. In addition, several minor problems with -z 3 statistics on
DNA sequences were fixed.
Added -m 9 option, which unfortunately does different things in
pvcompfa/sw and fasta3/ssearch3. In both programs, -m 9 provides the
id's of the two sequences, length, E(), %_ident, and start and end of
the alignment in both sequences. pvcompfa/sw provides this
information with the list of high scoring sequences. fasta3/ssearch3
provides the information in lieu of an alignment.
>>March 18, 1999
--> v32t02
Added information on the algorithm/parameter description line to
report the range of the pam matrices. Useful for matrices like
MD_10, _20, and _40 which require much higher gap penalties.
>>March 13, 1999 (not distributed)
--> v32t01
-r results.file has been changed to -R results.file to accomodate
DNA match/mismatch penalties of the form: -r "+1/-3".
>>February 10, 1999
Modify functions in scalesw*.c to prevent underflow after exp() on
Alpha Linux machines. The Alpha/LINUX gcc compiler is buggy and
doesn't behave properly with "denormalized" numbers, so "gcc -g -m
ieee" is recommended.
Add "Display alignments also (y/n)[n] "
pvcomplib.c again provides alignments!! In addition, there is a
new "-m 9" option, which reports alignments as:
>>>/home/wrp/slib/hlibs/hum0.aa#5>HS5 gi:1280326 T-cell receptor beta chain 30 aa, 30 aa vs /home/wrp/slib/hlibs/hum0.seg library
HS5 30 HS5 30 1.873e-11 1.000 30 1 30 1 30
HS5 30 HS2249 40 1.061e-07 0.774 31 1 30 7 37
HS5 30 HS2221 38 1.207e-07 0.833 30 1 30 7 35
HS5 30 HS2283 40 1.455e-07 0.774 31 1 30 7 37
HS5 30 HS2239 38 1.939e-07 0.800 30 1 30 7 35
where the columns are:
query-name q-len lib-name lib-len E() %id align-len q-start q-end l-start l-end
>>February 9, 1999
Corrected bug in showalign.c that offset reverse complement alignments
by one.
>>Febrary 2, 1999
Changed the formatting slightly in showbest.c to have columns line up better.
>>January 11, 1999
Corrected some bugs introduced into fastf3(_t) in the previous version.
>>December 28, 1998
Corrected various problems in dropfz.c affecting alignment scores
and coordinates.
Introduced a new program, fasts3(_t), for searching with peptide
sequences.
>>November 11, 1998
--> v32t0
Added code to correct problems with coordinate number in long library
sequences with tfastx/tfasty. With this release, sequences should be
numbered properly, and sequence numbers count down with reverse
complement library sequences.
In addition, with this release, fastx/y and tfastx/y translated
protein alignments are numbered as nucleotides (increasing by 3,
labels every 30 nucleotides) rather than codons.
./fasta-36.3.8h/doc/readme.v34t0 0000644 0001054 0001054 00000200177 13525131122 013467 0 ustar wrp
$Id: readme.v34t0 348 2010-07-20 21:33:22Z wrp $
$Revision: $
>>May 28, 2007
Small modification for GCG ASCII (libtype=5) header line.
>>January 12, 2007 fasta-34_26_2
Fix a problem with pssm_asn_subs.c reading strings (sequences) longer
than 1024 bytes.
Remove searchfa.cgi, searchnn.cgi, cgi-lib.pl, my-cgi.pl - this code
was used for an ancient FASTA WWW implementation and has been replaced
by the FASTA_WWW package.
FASTA Version numbers are being modified to make releases easier to
track, thus fa34t26b5 has become fasta-34_26_1. I would prefer to use
decimal versions, but CVS does not allow '.' in tags.
>>January 4, 2007 fasta-34_26_1
Include scripts for building Mac OS X Universal binaries on a PPC
machine. Programs are compiled first with Makefile.os_x (gcc-3.3 for
PPC) and then installed into ./ppc/. Programs are next compiled with
Makefile.os_x86 for i386, and the resulting executables installed into
./i386/. Finally, the "make_osx_univ.sh" script is run to build the
universal binaries from the two executables using "lipo".
>>December 12, 2006
Fix some problems with p2_workcomp.c: (1) no longer initialize pad
characters for non-existant sequences. (2) deal with small libraries
consistently with the serial versions.
>>November 17, 2006 fa34t26b5
Fixed a problem reading ASN.1 format 2 PSSM's. It is now possible to
download a PSI-BLAST PSSM RID and search properly. Next, the query
sequence from the PSSM should be used instead of the provided query
sequence, so that the query sequence is ignored.
>>October 19, 2006 fa34t26b4
Fixed problem with SSE2 code when PSSM's are used.
>>October 6, 2006 fa34t26b3
A new set of WIN32 programs is now available that use the Intel C++
9.1 compiler, rather than the much older Borland Turbo-C compiler. All
of the unthreaded programs that are part of the Unix and MacOSX FASTA
distributions are now available. Threaded (multiprocessor) versions
of the program as available as well, as are sse2 accelerated versions
of ssearch34 (ssearch34sse2.exe, ssearch34sse2_t.exe).
Th new WIN32 code also uses Microsoft's "nmake" program to build the
programs, which allows much greater consistency between the Unix and
Windows versions.
>>September 18, 2006
Static global alignment variables removed from dropnfa.c, dropfx.c,
dropfz2.c. dropnfa.c, dropfx.c and dropfz2.c should be thread safe.
Together with the earlier changes, all the FASTA functions should now
be thread safe during the alignment process.
>>August 17, 2006
Begin removal of static variables from Smith-Waterman alignment
functions. These variables kept the functions from being thread-safe.
Now dropgsw.c and dropnsw.c are thread-safe.
>>August 15, 2006 fa34t26b2
Fixed a problem with pv34compfx/mp34compfx (and fy) producing
improperly labeled alignments and de-allocating memory for the reverse
complement.
>>July 18, 2006
The library file name parsing programs now provide the option for
environment variable substitions. For example, SLIB2=/slib2 as an
environment variable (e.g. export SLIB2=/slib2 for ksh and bash), then
fasta34 -q query.aa '${SLIB2}/swissprot.fa' expands as expected.
While this is not important for command lines, where the Unix shell
would expand things anyway, it is very helpful for various
configuration files, such as files of file names, where:
<${SLIB2}/blast
swissprot.fa
now expands properly, and in FASTLIBS files the line:
NCBI/Blast Swissprot$0S${SLIB2}/blast/swissprot.fa
expands properly. Currently, Environment variable expansion only
takes place for library file names, and the >July 14, 2006 fa34t26b1
Updated Farrar smith_waterman_sse2.c code to address possible bug
(code from Michael Farrar). Include for
compilation with Sun compiler with Makefile.sun_x86.
>>July 2, 2006 fa34t26b0
This release provides an extremely efficient SSE2 implementation of
the Smith-Waterman algorithm for the SSE2 vector instructions written
by Michael Farrar. The SSE code speeds up
Smith-Waterman 8 - 10-fold in my tests, making it comparable to Eric
Lindahl's Altivec code for the Apple/IBM G4/G5 architecture.
The Farrar code is largely confined to smith_waterman_sse2.c and
smith_waterman_sse2.h, which are copyright (2006) by Michael Farrar,
and cannot be redistributed without his permission. Mr. Farrar has
agreed to provide his code under the same policy used by FASTA -
e.g. the code can be used without permission, but not redistributed.
The Farrar code uses GCC version 4.0 SSE2 intrinsic functions to avoid
assembly language code. Unfortunately, in my hands, "gcc -O3" causes
"out of memory" errors, and other problems, so "gcc -O" is used instead.
>>June 23, 2006 fa34t25d10
Modifications to comp_lib.c, compacc.c, and other files to ensure that
function-specific MAXTOT values are used properly. MAXTOT is now
available as m_msg.max_tot, which is set in initfa.c (m_msg.max_tot =
MAXTOT) to ensure that functions that need very large MAXTOT values
(e.g. TFASTX) can get them. tfastx can now search successfully with
titin, a 27,000 residue protein.
Other changes have been made to accomodate long query sequences.
A serious bug was found in fastx34(_t) that caused alignment
coordinates to be calculated improperly when the DNA sequence was much
longer than the protein sequence.
>>May 31, 2006 fa34t25d9
Fixed some problems with fasts/fastf alignments when -m 9 options were
used. Unlike the other algorithms, the a_res structure does not
capture all the information to re-produce an alignment, so do_walign
now sets bptr->have_ares to indicate whether the a_res structure is
valid.
Various problems with bad library names, and short query titles were
also fixed.
Updated version number/date on all drop*.c functions.
>>May 24, 2006 fa34t25d8
Revised code for NCBI *.pal/*.nal databases has been tested on all
architectures, including Windows.
In addition, support for ASN.1 PSSM:2 files provided by the NCBI
PSI-BLAST WWW site is included. This code will not work with
iteration 0 PSSM's (which have no PSSM information). For ASN.1
PSSM's, which provide the matrix name (and in some cases the gap
penalties), the scoring matrix and gap penalties are set appropriately
if they were not specified on the command line. ASN.1 PSSM's are type 2:
ssearch34 -P "pssm.asn1 2" .....
>>May 18, 2006
Support for NCBI Blast formatdb databases has been expanded. The
FASTA programs can now read some NCBI *.pal and *.nal files, which are
used to specify subsets of databases. Specifically, the
swissprot.00.pal and pdbaa.00.pal files are supported. FASTA supports
files that refer to *.msk files (i.e. swissprot.00.pal refers to
swissprot.00.msk); it does not currently support .pal files that
simply list other .pal or database files (e.g. FASTA does not support
nr.pal or swissprot.pal).
In the process of providing this support, the routines used to read
ASN.1 binary formatdb files were substantially improved. It is now
possible to see multiple description lines for a single sequence.
IS_BIG_ENDIAN has been removed from all of the Makefiles. The code
now looks for the definition of __BIG_ENDIAN__ or _BIG_ENDIAN to
decide whether the architecture IS_BIG_ENDIAN. If, for some reason,
one of these macros is not defined on a BIG_ENDIAN architecture, then
-DIS_BIG_ENDIAN is required.
>>May 12, 2006 CVS fa34t25d7
Corrected serious problem with coordinate display calculation for
fasta34 and ssearch34 - in some cases the coordinates and alignment
symbols were off by the length of the context (typically 30 residues).
Added capability to read ASN.1 binary PSSM information. This
information is provided (in an encoded form) from the NCBI PSI-BLAST
WWW site. (What is actually provided from the WWW site is a bzip2-ed
binary file that is converted to ASCII HEX. The ASCII HEX file must
be converted to binary, and then bunzip'ed. This bunzip-ed file is
binary ASN.1.) These files can also be generated by
blastpgp -J T -C pssm.asn1_bin -u 2
I am parsing the ASN.1 binary manually, not using the NCBI toolkit, so
there may be some files that are not parsed properly - if so, let me
know.
(May 12, 2006 - The NCBI changed the format of the psi-blast ASN.1
PSSM - and has not yet provided documentation of the new structure, so
this code does not work. It does work with blastpgp v 2.2.13, but not
with the web site version 2.2.14. A fix was provided 24-May-2006)
>>April 18, 2006
Small modification in mshowbest.c to provide more consistent display
widths with -m 9i in list of best hits.
>>April 11, 2006 CVS fa34t25d6
Corrected a problem introduced with the new, more efficient method for
displaying alignments. For the tfast* programs, which must translate
the library sequence, translations were not done when alignments were
re-displayed.
Corrected an older problem with tfastx34 against very long sequence
databases - the code to more efficiently do the display alignment did
not use the correct sequence coordinates.
Modifications to dropfs2.c to ensure that exact peptide matches are
captured more frequently.
>>March 16, 2006 CVS fa34t25d5
Change to initfa.c to allow lower case DNA libraries using the
-DDNALIB_LC compile time option.
Modify p2_complib.c, p2_worklib.c (and doinit.c, msg.h) to allow the
-V annotation option for the parallel programs. Also modify to allow
specification of the query range (but only for the first query, like
fasta34) for the parallel programs.
Modification of p2_workcomp.c to correct some problems presenting
percent similarity. Also correct unreleased bugs in the alignment
routines that allow more efficient alignment re-calculation.
>>Nov 20, 2005
Changes to support asymmetric matrices - a scoring matrix read in from
a file can be asymmetric. Default matrices are all symmetric.
>>Oct 24, 2005
Modifications extended to p2_complib.c/p2_workcomp.c. Incorporation
of drop_func.h into p2_workcomp.c greatly simplifies things. No
changes in communication - struct a_res_str is internal to
p2_workcomp.c.
Additional changes to do_walign() so that aln_func_vals() must be
called to set llfact, qlfact, etc in a_struct aln before or after
do_walign is called. do_walign produces a_res_str a_res, which has
all the information necessary to produce a calcons() or calc_code()
alignment.
>>Oct 19, 2005 CVS fa34t26b0
Modifications to drop*.c and c_dispn.c to separate (and simplify) some
of the alignment coordinate calculations. Before, the "a_struct" had
the coordinates of the alignment used in the display (seqc0, seqc1)
AND in the original sequences (aa0, aa1), as well as other information
used to calculate alignment coordinates. In the new version, astruct
coordinates always refer to seqc0,1, while a new structure, a_res_str,
has coordinates for aa0, aa1 as well as the alignment encoding in res[nres].
Eventually, this should make it possible to display multiple local
alignments from the same two sequences.
In addition, the file "drop_func.h" has been added to the project, and
is included by many of the files (all the drop*.c functions,
mshowbest.c, mshowalign.c) to ensure that the various functions are
declared and used consistently.
>>Sept 19, 2005 CVS fa34t25d4
Changes to support Mac OS 10.4 - Tiger (include sys/types.h in more
files). Documentation update for prss34/prfx34. Modifications to
comp_lib.c to support prss34_t/prfx34_t. Shuffle numbers for
prss/prfx can now be specified by "-k #".
>>Sept 2, 2005
The prss34 program has been modified to use the same display routines
as the other search programs. To be more consistent with the other
programs, the old "-w shuffle-window-size" is now "-v window-size".
prss34/prfx34 will also show the optimal alignment for which the
significance is calculated by using the "-A" option.
Since the new program reports results exactly like other
fasta/ssearch/fastxy34 programs, parsing for statistical significance
is considerably different. The old format program can be make using
"make prss34o".
>>Aug 26, 2005
Modifications to save_best() in comp_lib.c to support prss34_t. It
did not work before.
>>July 25, 2005
Modify mshowbest.c to suppress gi|12345 in HTML mode.
>>July 18, 2005 CVS fa34t25d3
Modifications to Makefile.tc to support NCBI formatdb formats under
Windows.
>>May 19, 2005 CVS fa34t25d2
Modifications to dropfs2.c to fix an obscure bug that occurred when
correctly ordered peptides aligned one residue apart.
>>May 5, 2005 CVS fa34t25d1
Modification to the -x option, so that both an "X:X" match score and
an "X:not-X" mismatch score can be specified. (This score is also used
give a positive score to a "*:*" match - the end of a reading frame,
while giving a negative score to "*:not-*".
>>March 14, 2005 CVS fa34t25b4
Fixed some problems caused by padding characters required for
Smith-Waterman ALTIVEC in the parallel (p2_complib.c, p2_workcomp.c)
versions.
>>Feb 24, 2005 CVS fa34t25b3
Changes to comp_lib.c (and Makefile.pcom) to support prss34_t.
>>Feb 12, 2005
Modify dropfs.c to dynamically allocate space for alignments, so that
queries with a large number of fragments can still place all the
fragments on the alignment. Also fix a problem produced by removing
-DBIGMEM from most of the Makefile's, but not fixing defs.h to use
BIGMEM sizes by default.
>>Jan 24, 2005
Include a new program, "print_pssm", which reads a blastpgp binary
checkpoint file and writes out the frequency values as text. These
values can be used with a new option with ssearch34(_t) and prss34,
which provides the ability to read a text PSSM file. To specify a
text PSSM, use the option -P "query.ckpt 1" where the "1" indicates a
text, rather than a binary checkpoint file. "initfa.c" has also been
modified to work with PSSM files with zero's in the in the frequency
table. Presumably these positions (at the ends) do not provide
information. (Jan 26, 2005) blastpgp actually uses BLOSUM62 values
when zero frequencies are provided, so read_pssm() has been modified
to use scoring matrix values for zero frequencies as well.
>>Jan 13, 2005
Change to initfa.c to have fasts34 do a protein comparison by default,
rather than an unknown sequence type. Automatic checking for fasts34
does not work reliably, because queries can be very short. Likewise
for fastm34. [Jan 26, 2004] Undo this change, which broke DNA
comparison when "-n" was specified.
>>Jan 7, 2005
Changes to tatstats.h, dropfs2.c to allow larger numbers of peptides
to match when fasts is used to show coverage on a proteomics
experiment. Previously fasts could match no more than 30 peptides,
that has been increased to 50. In addition, ktup=2 can be used
to increase the likelihood that short exact matchs trump longer
mismatched regions.
>>Nov 11, 2004 CVS fa34t25
Finished merge of earlier fa34t24 branch with HEAD. Correct
labeling of TFASTM.
>>Nov 4-8, 2004
Incorporation of Erik Lindahl "anti-diagonal" Altivec code for
Smith-Waterman, only. Altivec SSEARCH is now faster than FASTA for
query sequences < 250 amino acids.
Small modifications to output score display to ensure that the correct
scores are shown, and that they are correctly labeled.
>>Aug 25,26, 2004 CVS fa34t24b3
Small change in output format for p34comp* programs in
">>>query_file#1 string" line before alignments. This line is not present
in the non-parallel versions - it would be better for them to be consistent.
Change in last_stats.c to properly label fasts statistics with -z != 1.
Change in dropfs2.c to ensure that tatprobs are not precalculated with -z 4.
Modify -m 9i output option to show in HTML output.
Add "#ifdef NOOVERHANG" to dropfs2.c that causes overlapping
alignments to score a 0, rather than the partial overlap score.
Useful for SAGE alignments, because "fasts" requires global alignments
(except for for overhangs, unless NOOVERHANG is defined).
>>Aug 23, 2004
Fix problem with very long definition lines with formatdb version4
ASN databases. Fix mshowalign.c to re-enable "-L" option.
>>July 28, 2004
Fix to re-enable -w window shuffle for PRSS. Modify comp_lib.c
for PRSS to ensure that the unshuffled score and probability
are shown, even for very high probabililty alignments.
>>July 21, 2004
Modifications to support PostgreSQL databases with the same commands
as MySQL databases. MySQL database libraries are type 16, PostgreSQL
are type 17. Makefile.linux_sql and Makefile.pvm4_sql support both
database types simultaneously.
>>June 23, 2004 CVS fa34t24b2
Additional fixes to enable -n or -p with fasts34 and
fastm34. Makefile.pcom was fixed for fastm34_t. A new file,
mgstm1.nts, of DNA fragments from mgstm1.seq, is included for testing
fasts34 and fastm34.
>>May 4, 2004
Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM. This change
introduced a bug that broke FASTS completely, but was fixed June 18,
2004 (and retagged fa34t24b2).
>>April 23, 2004 CVS fa34t24b1
Fix bug in initfa.c that caused tfasts/tfastf not to examine all six
frames.
>>May 4, 2004
Fixes to initfa.c to allow DNA:DNA for FASTS, FASTM.
>>March 19, 2004 CVS fa34t24b0
Modify all the drop*.c files, plus mshowbest.c and mshowalign.c, to
display percent similarity, rather than percent ungapped. An
alignment is counted as similar if the score is greater than or equal
to zero (the same criterion used for placing ".". To disable this
change, remove -DSHOWSIM from the appropriate Makefile.*.
>>March 18, 2004 CVS fa34t23b8
Fix bug in initfa.c tables that caused prss to generally compare
proteins.
>>March 15, 2004
Fix bug in calls to revcomp(); make revcomp() guarantee NULL termination.
>>March 2, 2004 CVS fa34t23b7
Fix a very embarrassing and surprising bug that caused insertions
in fasta alignments to appear in the wrong sequence.
>>Feb 7, 2004 CVS fa34t23b6
Change initfa.c to allow "-i" (reverse complement) and "-i -3" with
"fastx34" and "prfx34". In addition, "prfx34" now examines both query
DNA strands in calculated the shuffled statistical significance.
>>Feb 5, 2004
Reverse assignments for G:U baseparing in initfa.c.
Fix memory allocation error caused by doubling DNA alignment width.
>>Jan 7, 2004 CVS fa34t23b5
Change in do_walign() in dropnfa.c to make final DNA alignments use a
band that is 2X as large as the search band width.
>>Dec 22, 2003 CVS fa34t23b4
Fix typo in p2_complib.c that prevented compilation. Fix problem
with karlin.c for asymmetrical matrices, such as used with -U.
>>Dec 10, 2003 CVS fa34t23b3
Fix problem in resetp()/initfa.c that disabled banded Smith-Waterman
DNA alignments.
Allow spam() to do extended alignments for DNA if one of the sequences
is < 50 nt.
Cause default ktup to drop for short sequences. For protein < 50, ktup=1;
for DNA < 20, 50, 100 ktup = 1, 2, 3, respectively.
>>Dec 7, 2003
A new option, "-U" is available for RNA sequence comparison. "-U"
functions like "-n", indicating that the query is an RNA sequence. In
addition, to account for "G:U" base pairs, "-U" modifies the scoring
matrices so that a "G:A" match has the same score as "G:G" match,
and "T:C" match has the same score as a "T:T" match. (Corrected
13-July-2010 -- the G:A/T:C scores are score(G:G)-3.) The asymmetric
matrix required changes in dropnfa.c that were similar to the changes
in dropgsw.c required for profiles. In addition, m_msg.qdnaseq and pst.dnaseq
can now be SEQT_DNA, SEQT_RNA, SEQT_PROT, SEQT_UNK, or SEQT_OTHER.
m_msg.ldnaseq does not use SEQT_RNA, only SEQT_DNA. A new member of
struct pstruct: int nt_align, is used to indicate nucleotide
alignments.
>>Nov 19, 2003
Changes to Makefile's to distinguish between tatstats_fs.o and
tatstats_ff.o.
>>Nov 2, 2003
Substantial changes to comp_lib.c, p2_complib.c, mshowbest.c, and
mshowalign.c to support more sophisticated display options.
Previously, one could have only on "-m #" option, even though several
of the options were orthogonal (-m 9c is independent of -m 1 and -m2,
which is independent of -m 6 (HTML)). The programs now use a bitmask
that allows independent options to be combined. In particular -m 9c
can be combined with -m 6, which can be very helpful for runs that
need HTML output but can also exploit the encoding provided by -m 9c.
The "-m 9" option now also allows "-m 9i", which shows the standard
best score information, plus percent identity and alignment length.
>>Oct 26, 2003 CVS fa34t23b1
Additional fixes to Makefiles to enable tfastf34(_t). Changes to
support ossearch34 (a non-Phil Green optimized Smith-Waterman).
>>Oct 8, 2003 CVS fa34t23b0
Fixes to get DNA queries working in both directions, and to fix PCOMPLIB
programs for "-V" option. Currently, the parallel programs cannot use
the "-V" option.
>>Sept 25, 2003
A new option is available for annotating alignments. -V '@#?!'
can be used to annotate sites in a sequence, e.g:
>GTM1_HUMAN ...
PMILGYWDIRGLAHAIRLLLEYTDS@S?YEEKKYT@MG
DAPDYDRS@QWLNEKFKLGLDFPNLPYLIDGAHKIT
might mark known and expected (S,T) phosphorylation sites. These
symbols are then displayed on the query coordinate line:
10 20 @? 30 @ 40 @ 50 60
GTM1_H PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
gtm1_h PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLP
10 20 30 40 50 60
This annotation is mostly designed to display post-translational
modifications detected by MassSpec with FASTS, but is also available
with FASTA and SSEARCH.
>>Sept 22, 2003 CVS fa34t22b5
The Altivec Smith-Waterman code has been removed.
>>Sept 17, 2003 CVS fa34t22b4
A variety of different bugs have been fixed. (1) All the functions in
the old initsw.c are now in initfa.c; initsw.c will be removed.
Specifically, the Profile/PSSM code is now in initfa.c. initfa.c is
now fully table driven. (2) various problems with prss34 and prfx34
have been fixed in initfa.c. (3) An additional ncbl2_mlib.c buffer
overrun has been fixed. (4) fastf34 is now available in this package.
Its performance is very similar to, but not identical to, fastf33. I
am tracking down the differences. In general, the raw scores
calculated by both programs are the same, but the statistical analysis
seems to be slightly different.
>>July 30, 2003 CVS fa34t22b3
Fix bug in ncbl2_mlib.c that caused buffer overrun with blast/formatdb
v3 description lines.
>>July 28, 2003
The initfa.c file has been substantially re-structured to use a
table-driven approach to parameter setting, rather than the previous
confusing combinations of #ifdef's. Two tables of parameters are
used, pgm_def_arr[] and msg_def_arr[], which specify values like the
program name, reference, scoring matrix, default gap penalties, etc.
msg_def_arr[] has the sequence types for the query, library, and
algorithm, as well as other parameters (qframe, nframe, nrelv, etc),
which greatly simplifies the sequence recognition logic. ppst->pgm_id
can be used to identify the program that is running. Eventually,
almost all of the program specific #ifdef's will be removed from
initfa.c. initfa.c now provides initsw.c functionality, so that
initsw.c is no longer needed.
>>July 25, 2003
A new file is included - fasta.defaults - that lists the scoring
matrix, gap penalty, and other defaults for all of the fasta34
programs. This file will be used soon to simplify parameter setting
for the FASTA programs, and should also be used by Javascript WWW
interfaces to the FASTA programs.
>>July 22, 2003 CVS fa34t22b2
Fixes to dropfs2.c, tatprobs.c to ensure that negative probabilities
cannot occur. Negative probabilities were never seen with standard
matrices, but did occur with BL50. Another optimization in dropfs.c
considerably improves fasts34 performance in some cases.
Fix a problem with formatdb v4 ASN.1 format files.
>>July 12, 2003
Fix a bug that prevented "-L" (long sequence descriptions) from
working.
>>July 9, 2003
Fix reverse complement (M:K) error. Fix off-by-one error for FASTA
DNA alignments that caused the first aligned residue pair to be
missed.
>>July 4 - 8, 2003
Incorporate blast-def-line ASN.1 parsing so that NCBI formatdb version
4 files can be read.
>>June 26, 2003
The strategy for displaying the match/mismatch line (" .:" for -m 0)
has been changed dramatically to acommodate more sophisticated
strategies for indicating conservative replacements, e.g. because of
PSSM's. In addition to seqc0 and seqc1, which hold the aligned
sequences for display, there is also seqca, which holds the alignment
symbol. calcons(), do_show(), and discons() have all changed to
include seqca. calcons() is somewhat more complex; discons() is much
simpler. (June 29, 2003 - dropgsw.c calcons() now displays profile
similarity accurately - it is very very illuminating.)
>>June 16, 2003 version: fasta34t22
ssearch34 now supports PSI-BLAST PSSM/profiles. Currently, it only
supports the "checkpoint" file produced by blastall, and only on
certain architectures where byte-reordering is unnecessary. It has not
been tested extensively with the -S option.
ssearch34 -P blast.ckpt -f -11 -g -1 -s BL62 query.aa library
Will use the frequency information in the blast.chkpt file to do a
position specific scoring matrix (PSSM) search using the
Smith-Waterman algorithm. Because ssearch34 calculates scores for
each of the sequences in the database, we anticipate that PSSM
ssearch34 statistics will be more reliable than PSI-Blast statistics.
The Blast checkpoint file is mostly double precision frequency
numbers, which are represented in a machine specific way. Thus, you
must generate the checkpoint file on the same machine that you run
ssearch34 or prss34 -P query.ckpt. To generate a checkpoint file,
run:
blastpgp -j 2 -h 1e-6 -i query.fa -d swissprot -C query.ckpt -o /dev/null
(This searches swissprot for 2 iterations ("-j 2" using a E()
threshold 1e-6 saving the resulting position specific frequencies in
query.ckpt. Note that the original query.fa and query.ckpt must
match.)
>>June 5, 2003
Fix to mshowbest.c to get -m 9 coordinates correct on reverse strand
with pv34comp*. Some additional fixes for prfx34.
>>May 22, 2003
Changes to llgetaa.c, getseq.c, comp_lib.c to provide a different
library residue lookup table (sascii) for queries and libraries. This
allows one to make a prfx34 (like prss34, but using the fastx
algorithm). prfx34 is now available.
>>May 13,14 2003
Fixes to most of the drop*.c files, and mshowbest.c, to ensure that
coordinates displayed with -m 9(c) and the final alignment are
consistent. They were consistent for fasta34/ssearch34/fasts34, but
not for fastx34/fasty34. The alignment coordinate system has been
been revised for consistency in allthe drop*.c programs (coordinates
used to be off-by-one for some, but not other functions).
Fixes to -m 9c for fasty34/pv34compfy. In addition, a problem was
fixed with fastx34/fasty34 that appeared with a protein sequence was
considerably longer than the DNA query, e.g. an EST vs titin (26K
residues). This problem only appeared on pv34compfx/fy on Xserve's
under OS_X; but it should improve fastx34/fasty34 performance with
very long protein sequences on all platforms.
>>May 7,8 2003
Changes to p2_workcomp.c, compacc.c, and p_mw.h to fix persistent
bugs in the -m 9c display. Previous pv34comp* programs would not
return the correct coded alignment if more than 100 alignments came
from the same node, or if an encoding was longer than 127 chars.
Also, fixes to p2_complib.c, comp_lib.c, to allow long query sequences
to be segmented. Previously, only the first 20,000 residues were
used. The segmented queries are not overlapped; segmented library
sequences are.
>>May 5, 2003
Changes to last_tat.c, scaleswt.c to ensure that all fasts alignments
that are likely to have significant scores are displayed. In previous
implementations, if the query had more than 10 fragments, only the 100
best scores were shown. Now, we rescore up to 2500 alignments. The
new approach allows large mixtures to be used for searches, where some
of the fragments from the mixture match too many proteins
(e.g. actins). Some differences between the fasts34 and pv34compfs
implementations have been fixed. The two programs typically will not
give exactly the same results, because of small differences in the
sampling procedures, but the results are essentially equivalent.
>>Apr 11, 2003 CVS fa34t21b3
Fixes for "-E" and "-F" with ssearch34, which was inadvertantly disabled.
A new option, "-t t", is available to specify that all the protein
sequences have implicit termination codons "*" at the end. Thus, all
protein sequences are one residue longer, and full length matches are
extended one extra residue and get a higher score. For
fastx34/tfastx34, this helps extend alignments to the very end in
cases where there may be a mismatch at the C-terminal residues.
-m 9c has also been modified to indicate locations of termination
codons ( *1).
>>Mar 17, 2003 CVS fa34t21b2
A new option on scoring matrices "-MS" (e.g. "BL50-MS") can be used to
turn the I/L, K/Q identities on or off. Thus, to make "fastm34" use
the isobaric identities, use "-s M20-MS". To turn them off for "fasts34",
use "-s M20".
More fixes for correct alignment coordinates. There was a conflict between
-m 9 and -m 9c and subsequent alignment displays.
>>Mar 13, 2003
Various fixes to produce correct fastm34 alignments. Changes to all
functions to correct potential problem with -m 9 alignment coordinates
when both -m 9 and actual alignments are shown.
>>Feb 25,27, 2003
Modifications to re-activate showsum.c, which included corrections to
the showbest() call in p2_complib.c.
>>Feb 13, 2003 CVS fa34t21b1
Modifications to dropfx.c to dramatically improve alignment speed for
cases where the DNA sequence is considerably longer than the protein
sequence. Previously, a 200 aa vs 5000 nt comparison would do a full
200 x 5000 Smith-Waterman alignment; with this modification, no more
than a 200 x 1200 (2x3x200) alignment is done. This optimization has
not (yet) been applied to dropfz2.c (fasty/tfasty).
>>Feb 11, 2003
Small modifications to comp_lib.c, p2_complib.c, and nmgetlib.c to
pass openlib() a possibly old lmf_str. This allows openlib() to
re-use memory mapped files. closelib() no longer releases memory
mapped file buffers. Under Linux, memory mapped file buffers were not
really released, so when comparing a set of sequences against nr, the
program could not mmap() the database after several searches. This
will also speed up memory mapped multiple sequence searches.
>>Jan 28-31, 2003 CVS fa34t21b0
Fix another bug (all of v34t20) involved with overlapping long
sequences. And another bug that occurred when using sampled
statistics, but appeared only on the SGI platform - thanks to Dmitri
Mikhailov. Several other issues have been addressed based on more
instrumented runtime testing.
Fix an old (all v34) bug that caused problems with -z 11-16 (shuffled
sequence array was not allocated properly). Fixed another bug with -z
6/16 when using threaded (_t) searches in fasta34_t.
Restructure statistical analysis functions (scaleswn.c, scaleswt.c) to
return the "final" statistical estimation routine done in pst.zsflag_f.
This allows the program to cope with searches against a single sequence
correctly.
Corrected an error for DNA sequences needing Altschul-Gish statistics.
>>Jan 25, 2003
Add option "-J start:stop" to pv34comp*/mp34comp*. "-J x" used to
allow one to start at query sequence "x"; now both start and stop can
be specified.
>>Jan 14, 2003
Changes to apam.c to provide an error message on stderr when a scoring
matrix cannot be found.
Changes to dropfs2.c, initsw.c, initfa.c to provide -m9c information
for fasts34 searches. Modify the alignment algorithm to use
probabilistic scores properly.
>>Dec 22, 2002
Change to compacc.c (sortbeste()) to do a second sort on zscore when
several sequences have E() == 0.
>>Nov 27, 2002
Change FSEEK_T to fseek_t to keep Borland BCC5 happy.
>>Nov 14-22, 2002 CVS fa34t20b6
Include compile-time define (-DPGM_DOC) that causes all the fasta
programs to provide the same command line echo that is provided by the
PVM and MPI parallel programs. Thus, if you run the program:
fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12
the first lines of output from FASTA will be:
# fasta34_t -q gtt1_drome.aa /slib/swissprot
FASTA searches a protein or DNA sequence data bank
version 3.4t20 Nov 10, 2002
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
This has been turned on by default in most FASTA Makefiles.
Fix p2_complib.c so that qstats[] is always allocated before it is used.
Fix serious bug in non-threaded comp_lib.c that caused some high
scoring sequences to be missed by fasts34. New tests are included in
test.sh to detect this problem in the future.
The shell sort algorithm in sortbeste(), sortbestz(), and sortbesto()
has been modified to use an improved algorithm that will not go
quadratic in pathological cases.
nmgetlib.c and mmgetaa.c have been modified to remove "^A" in libstr
when used with p2_complib.c.
Fix problem with MAXSEG in tatstats.h with IBM/AIX.
Changes to most Makefiles to use -DSAMP_STATS; fixes to p2_complib.c
for SAMP_STATS.
>>Oct 22, Nov 3, Nov 9, 2002 CVS tag fa34t20b5
Fix problem in comp_lib.c that caused the query sequence length to be
counted twice.
Fixed problem with prss34 (updated find_zp in showrss.c).
Correct shuffling function in several places.
Add jitter back to addhistz() - improves appearance with prss34.
Changes to fix problems with aln_code using -m 9c.
Fix to serious bug in scaleswt.c (fasts34, etc) that caused sorts on
the high scores to take much to long. The program is now 10X faster,
and scales well on PVM/MPI.
Fix to llgetaa.c to work with new getseq() API with automatic alphabet
recognition.
>>Oct 12, 2002 CVS tag fa34t20b4
Several very obscure (and sometimes old) bugs that appeared in certain
MPI environments have been fixed. This occurred because the pst.sq[]
array did not always have a '\0' at the end. In addition,
mshowalign.c/p2_workcomp.c sometimes failed to put the '\0' at the end
of seqc0/seqc1. Correct bug introduced in fa34t20b3 for fasts34(_t).
>>Oct 9, 2002 CVS tag fa34t20b3
Fix to apam.c build_xascii() to not zero-out qascii[0]. Fix
Makefile.pvm4. Mix problem with -m 9c with compacc.c.
>>Sept 28, 2002
Additional fixes to -m 9c in p2_complib.c/compacc.c/mshowbest.c.
Remove restriction in fasts34(_t) to less than 30 peptides (though no
more than 30 peptides can be aligned currently).
>>Sept 24, 2002
Fix p2_workcomp.c so that e_scores are delivered correctly when
last_calc flag is set, and -m 9c provides alignments when only one
best hit is present.
Fix comp_lib.c to use different maxn and overlap for each different
query sequence. fasta34 and fasta34_t now have identical results when
a long sequence is searched.
Add '@C:101' support to memory mapped FASTA format files.
Fix mshowalign.c so that coordinates returned by cal_coord() use
loffset+l_off.
>>Sept 14, 2002 CVS tag fa34t20b2
Changes to p2_complib.c, compacc.c to fix statistics problems with
pv34compfs on query sequences with more than 10 fragments.
>>Aug 27, 2002
Modifications to mshowbest.c and drop*.c (and p2_workcomp.c,
compacc.c, doinit.c, etc.) to provide more information about the
alignment with the -m 9 option. There is now a "-m 9c" option, which
displays an encoded alignment after the -m 9 alignment information.
The encoding is a string of the form: "=#mat+#ins=#mat-#del=#mat".
Thus, an alignment over 218 amino acids with no gaps (not necessarily
100% identical) would be =218. The alignment:
10 20 30 40 50 60 70
GT8.7 NVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQ
:.:: . :: :: . .::: : .: ::.: .: : ..:.. ::: :..:
XURTG NARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQ
20 30 40 50 60
would be encoded: "=23+9=13-2=10-1=3+1=5". The alignment encoding is
with respect to the beginning of the alignment, not the beginning of
either sequence. The beginning of the alignment in either sequence is
given by the an0/an1 values. This capability is particularly useful
for [t]fast[xy], where it can be used to indicate frameshift positions
"/#\#" compactly. If "-m 9c" is used, the "The best scores" title
line includes "aln_code".
>>Aug 14, 2002 CVS tag fa34t20
Changes to nmgetlib.c to allow multiple query searches coming from
STDIN, either through pipes or input redirection. Thus, the command
cat prot_test.lseg | fasta34 -q -S @ /seqlib/swissprot
produces 11 searches. If you use the multiple query functions, the
query subset applies only to the first sequence.
Unfortunately, it is not possible to search against a STDIN library,
because the FASTA programs do not keep the entire library in memory
and need to be able to re-read high-scoring library sequences. Since
it is not possible to fseek() against STDIN, searching against a STDIN
library is not possible.
>>Aug 5, 2002
fasts34(_t) and fastm34(_t) have been modified to allow searches with
DNA sequences. This gives a new capability to search for DNA motifs,
or to search for ordered or unordered DNA sequences spaced at
arbitrary distances.
>>Aug 4, 2002
comp_lib.c has been modified to provide comp_mlib.c function.
comp_mlib.c is no longer used. comp_lib.c with the "mlib" function
can now recognize protein or DNA sequences automatically, and reads
from stdin can now detect DNA/protein sequence types automatically.
Changes to compacc.c, getseq.c, doinit.c initfa.c, initsw.c, and
nmgetlib.c to support automatic sequence type detection.
>>July 28-31, 2002
(1) The various Makefile's have been "normalized". The fast*34[_t]
(Makefile.34m.common[_sql]), Makefile.pvm4[_sql], and
Makefile.mpi4[_sql] make files all use a common set of filenames,
described in Makefile.fcom. This greatly simplifies adding
programs, but requires that all *.o files be deleted when moving
from fast*34* to pv34comp* to mp34comp*.
(2) showalign.c/p_showalign.c have been merged into mshowalign.c
showbest.c/manshowbest.c have been merged into mshowbest.c. Some
of the related files (showun.c, manshowun.c, have not been merged
or tested).
(3) Code for ranking scores with valid e_value's incorporated.
(4) Bug fixes in p2_complib.c, so that fasts34/fasts34_t/pvcompfs
provide identical statistics.
>>July 26, 2002
Makefile.pvm4_sql and Makefile.pvm4 have been substantially simplified
by providing the worker program name from the h_init() function in the
initfa.c/initsw.c files.
>>July 24, 2002
Substantial modifications to param.h, structs.h to ensure that no
sequence specific information is kept in struct pstruct. This
structure now holds the pam[] matrix, and other scoring parameters,
but nothing that is dependent on aa0. The aa0 dependent stuff (nm0,
Lambda, K, etc) is now stored in struct mngmsg. This was mostly done
to support the pv34comp* programs, which have separate mngmsg
structures but the same pstructs.
The fasts34, fasts34_t, and pv34compfs/c34.workfs have all been tested
successfully.
>>July 19, 2002
Fix an old bug in the calculation of E()-values in DNA databases
longer than 2147483647 residues on machines with 32-bit longs.
>>July 28-31, 2002
(1) The various Makefile's have been "normalized". The fast*34[_t]
(Makefile.34m.common[_sql]), Makefile.pvm4[_sql], and
Makefile.mpi4[_sql] make files all use a common set of filenames,
described in Makefile.fcom. This greatly simplifies adding
programs, but requires that all *.o files be deleted when moving
from fast*34* to pv34comp* to mp34comp*.
(2) showalign.c/p_showalign.c have been merged into mshowalign.c
showbest.c/manshowbest.c have been merged into mshowbest.c. Some
of the related files (showun.c, manshowun.c, have not been merged
or tested).
(3) Code for ranking scores with valid e_value's incorporated.
(4) Bug fixes in p2_complib.c, so that fasts34/fasts34_t/pvcompfs
provide identical statistics.
>>July 26, 2002
Makefile.pvm4_sql and Makefile.pvm4 have been substantially simplified
by providing the worker program name from the h_init() function in the
initfa.c/initsw.c files.
>>July 24, 2002
Substantial modifications to param.h, structs.h to ensure that no
sequence specific information is kept in struct pstruct. This
structure now holds the pam[] matrix, and other scoring parameters,
but nothing that is dependent on aa0. The aa0 dependent stuff (nm0,
Lambda, K, etc) is now stored in struct mngmsg. This was mostly done
to support the pv34comp* programs, which have separate mngmsg
structures but the same pstructs.
The fasts34, fasts34_t, and pv34compfs/c34.workfs have all been tested
successfully.
>>July 8, 2002
Modifications to comp_lib.c, initfa.c and new scaleswt.c, tatstats.c
to support FASTS with Tatusov statistics.
last_params() has been introduced to allow aa0 dependent changes in m_msg/pstr.
sortbest() has been moved into initfa.c/initsw.c to make it function specific.
find_z() takes an additional parameter, escore.
The do_work() results structure, beststr, and stat_str all accommodate
escores as well as integer scores (stat_str also saves segn and segl
but doesn't need them).
In scaleswt.c, process_hist() now knows much more about Tatusov statistics.
last_stats() provided to accommodate rank-based statistical corrections.
scale_scores() is the last function to modify the beststr scores
(final calculation of E-value).
Some sortbest*() calls and some bptr[i]->zscore=find_zp() loops have
been moved into scale_scores();
>>July 3,5, 2002
Modifications to allow mySQL comments (--) in "library.sql 16" files.
Thus, a first line of:
--host seqdb user password;
is read by FASTA as the login information to a mySQL server, but is
ignored by mySQL. "DO" commands in FASTA mySQL files can also be
rendered invisible to mySQL in this way. See "do.sql".
Modifications to mysql_lib.c to allow very long SQL statements. The
buffer is now dynamically reallocated in 4Kb chunks.
The fasta3.1 man page has been updated and re-organized.
>>June 26, 2002
Minor modifications to nmgetaa.c (openlib()) to use the same arguments
for searching and PRSS. PRSS needs access to all of m_msg, but
searches do not. Other small fixes to comp_mlib.c, towards the goal
of merging comp_mlib.c and comp_lib.c.
>>June 25, 2002
Modify the statistical estimation strategy to sample all the sequences
in the database, not just the first 60,000. The histogram is still
based only on the first 60,000 scores and lengths, though all scores
an lengths are shown. The fit to the data may be better than the
histogram indicates, but it should not be worse.
Currently, this modification is available only if the -DSAMPLE_STATS
option is defined.
>>June 23, 2002 CVS fa34t11d4
Fix a very long-standing bug in fasty/tfasty that caused 'NNN' to be
translated as 'S', rather than 'X'. fastx/tfastx has done this
correctly for many years, but the fasty/tfasty code that I received
from Zheng Zhang was not implemented correctly (my fault, his code was
fine).
>>June 19, 2002
Added "-C #" option, where 6 <= # <= MAX_UID (20), to specify the
length of the sequence name display on the alignment labels. Until
now, only 6 characters were ever displayed. Now, up to MAX_UID
characters are available.
>>May 30, 2002 CVS fa34t11d3
Fixed problem with programs using the default -E cutoff when -b was
provided. With this implementation, -E can override -b, but -b
overrides the default -E.
Fixed problem with 64-bit file offsets in param.h (change USE_FSEEK0
-> USE_FSEEKO, include -D_LARGEFILE_SOURCE and -D_LARGEFILE64_SOURCE
in Makefile.linux_sql). Put limits on alignment display length (200
chars). More checks for null returns from SQL queries.
>>Apr 17, 2002 CVS fa34t11d2
Fixed bug in mm_file.h/ncbl2_mlib.c that caused the SGI version to be
unable to read blast2 format files.
Changed "mp_*" tags to "pg_*" for -m 10 option.
>>Mar 30, 2002
Fix embarrassing bug in revcomp() (getseq.c) that failed to complement
the central nucleotide in a sequence with an odd number of residues.
Small changes to dropfs.c for more segments.
>>Mar 16, 2002
Added create_seq_demo.sql, nt_to_sql.pl to show how to build an SQL
protein sequence database that can be used with with the mySQL
versions of the fasta34 programs. Once the mySQL seq_demo database
has been installed, it can be searched using the command:
fasta34 -q mgstm1.aa "seq_demo.sql 16"
mysql_lib.c has been modified to remove the restriction that mySQL
protein sequence unique identifiers be integers. This allows the
program to be used with the PIRPSD database. The RANLIB() function
call has been changed to include "libstr", to support SQL text keys.
Due to the size of libstr[], unique ID's must be < MAX_UID (20)
characters.
A "pirpsd.sql" file is available for searching the mySQL distribution
of the PIRPSD database. PIRPSD is available from
ftp://nbrfa.georgetown.edu/pir_databases/psd/mysql.
>>Mar 6, 2002
Fix showbest.c showbest() to report pst.zdb_size as database size.
Fix dropnfa.c spam() to address off-by-one on end of run, and double
counting on backwards scan. Fix dropnfa.c do_fasta() to fix another
problem introduced by -S. Changes to comp_lib.c to ensure that both
the beginning and end of the query and library sequence have '\0'
present. Changes to initfa.c, initsw.c to ensure that a match to a
lower-case letter with -S gets exactly the same score as a match to an
'X'. Changes to mmgetlib.c to work with 64-bit longs in *.xin files.
>>Feb 26, 2002
Fixes to doinit.c, initfa.c, initsw.c to allow DNA matrices using the
"-s dna.mat" option. A new matrix, "d50ry.mat" is available that
scores +5 for a match, -2 for a transition, and -5 for a
transversion. "d50ry.mat" corresponds to DNA PAM50 with transitions
twice as common as transversions. When "-s dna.mat" is used, "-n"
MUST be used as well.
Query sequence names ("aa", "nt") should be more accurate.
>>Feb 22, 2002
Fix to getseq.c to allow "plain" sequence files.
>>Feb 12, 2002
Minor fix to res_stats.c.
>>Jan 28, 2002
Fixes to resurrect res_stats.c. res_stats (cc -o res_stats
res_stats.c scaleswn.c -lm) takes the output from a current "-R
file.res" file and calculates statistical significance - this allows
one to take exactly the same set of scores (and lengths) and calculate
statistical estimates using different strategies.
>>Jan 24, 2002
modifications to mmgetlib.c, ncbl2_mlib.c to more robustly read memory
mapped files (*.xin, map_db) on machines lacking "native" 64-bit
longs. If the machine provides some definition for a 64-bit long
(e.g. "long long", "int64_t"), things should work. 64-bit offsets into
memory mapped files work properly on Alpha, SGI, i386 Linux, and
MacOSX. The current implementation depends either on 64 bit longs
(Compaq Alpha's pre 4.0G) or the file. Makefile,
Makefile.alpha, and Makefile.linux have been modified.
Modifications to nmgetlib.c, mmgetlib.c to provide GI numbers and
Accession versions for Genbank searches. If the GI:123456 number is
available, it will be used and the description line will be formatted:
gi|123456|gb|ACC1234.1|LOCUS description
This should help FAST_PAN runs, where the version of a sequence
changes frequently.
>>Jan 10, 2002
Modifications to p2_complib.c, p2_workcomp.c to more reliably allocate
space for library sequence descriptions on the master and workers.
>>Jan 2-3, 2002 CVS fa34t10c/fa34t10d3
Fixes to comp_lib.c to support Macintosh and Windows/Turbo-C
compilation. New Makefile.tc. Macintosh version supports both
"Classic" and "Carbon" environments.
"" has been replaced with the more modern ""
Fixes to p2_complib.c to support n_libstr (libstr length) in GETLIB().
comp_thr.c, complib.c removed.
>>Dec 16, 2001
Complete integration of comp_mlib.c with both the unthreaded and
threaded programs. Comp_mlib allows fasta34 and fasta34_t to compare
a database with a second database, just as pv34compfa does. Using
multiple queries with fasta34_t is not as efficient as pv34compfa (and
it cannot use networks of Unix workstations), but it is much easier to
use and install.
With the comp_mlib.c option, fasta34 cannot automatically recognize
DNA sequences, just as pv34compfa no longer recognizes DNA sequences.
You must use the "-n" option to search with DNA sequences. The other
programs (fastx34, tfastx34, etc) "know" the type of the query and
database sequences, so "-n" is only required for fasta34(_t).
>>Dec 14, 2001 CVS tag fa34t10b
Fix problems reading DNA databases in blast2 format.
>>Dec 11, 2001
Changes to spam() in dropnfa.c so that, for DNA sequences, the
previous behavior for finding the boundaries of a local alignment
region use the same algorithm as previous versions of fasta. For
protein sequences, the algorithm will extend the local region beyond
the "ktup" boundaries if a better score can be found. For DNA
sequences, this raises the noise rather than increasing sensitivity,
so it is turned off and "ktup" boundaries are respected. The old,
"ktup" boundary algorithm is available with -DNOSPAM_EXT.
This version also includes a working res_stats.c, which can be used to
test various statistical estimates on exactly the same set of scores.
Fixed problems with -m 9 percent identity for fastx/fasty/tfastx/tfasty.
These errors have been present since -m 9 was implemented.
>>Dec 10, 2001
Fix to map_db.c to work correctly with files > 2 Gb when 64-bit longs
are available. It is not yet designed to work with ftello() and other
offset types.
>>Nov 11,21, 2001 CVS tag fa34t10a, fa34t10d1
Substantial changes to revcomp(), getseq(), and other functions to
correct problems with -S on DNA sequences. Sequences with lower case
nucleotides were not recognized or reverse complemented properly.
Fix to dropnfa.c (v34t07, Nov 21, 2001) bg_align() to re-initialize
static globals - this fixes a problem encountered with pv34compfa. A
new main program, comp_mlib.c has been added to the CVS archive,
although it is not referenced in any of the Makefile. comp_mlib.c
works like p2_complib.c and compares a library against another
library.
>>Nov 4, 2001
Change to dropnfa.c spam () while(1) -> while(lpos <= dmax->stop).
This fixes a problem with ktup=1 on Suns only, so far.
>>Oct 4, 2001 CVS tag fa34t10
Add comp_lib.c file, which merges complib.c (unthreaded) and
comp_thr.c (threaded) code into one file.
Modifications to nmgetlib.c, mmgetaa.c to allow Genbank flatfile
format without DESCRIPTION or ACCESSION lines.
Additional fix for -S with ktup=1.
>>Sept. 24, 2001
Fix to have correct gap-penalties for short scoring matrices with
tfastx/fastx.
>>Sept. 10, 2001 CVS tag fa34t05d6
Fix a bug introduced by -S fix in fa34t05d5. Also, try to remove
changes in p34compfa compared to pv4compfa output.
>>Sept. 6, 2001 CVS tag fa34t05d5
Fix the -S dropnfa/fx/fz2 bug that was not actually fixed in
fa34t05d4. Incorporate the correct scaleswn.c refered to in
fa34t05d4.
>>Sept. 5, 2001 CVS tag fa34t05d4
Fix problem with m_msg.quiet that prevented interactive prompts for
ktup, file name, etc with threaded programs.
Fix serious bug in dropnfa.c/dropfx.c/dropfz2.c that caused -S to work
improperly on sequences with effective length of 3 or less.
Change to scaleswn.c to make mle_cen(), mle_cen2() more robust to cases
where the top and bottom scores are the same.
Change p2_complib.c to avoid compiler complaints with (void *)wstage2p=NULL
on some platforms.
>>Aug. 30, 2001 CVS tag fa34t05d3
Fixed problem with uthr_subs.c for Suns, but changed Makefile.sun to
use pthreads rather than Sun Unix threads. Removed SQL stuff from
Makefile.mpi4/pvm4 and added Makefile.mpi4_sql/pvm4_sql.
fa34t05d2 - fix to map_db.c to provide *sascii.
fa34t05d1 - fixes to ibm_pthr_subs.c and Makefile.ibm from IBM.
>>Aug. 20, 2001 CVS tag fa34t05d0
The pvm/mpi complib programs have been substantially updated with
release 3.4. See readme.v34t0 for more information. With version
3.4, the MPI programs are mp34comp*, mu34comp*, etc.
A major effect of this change is to disable automatic sequence type
(protein/DNA) recognition with pv34compfa/mp34compfa. By default,
protein libraries are assumed. Thus, pv34compfa/mp34compfa require
the "-n" command line option when running pv34compfa/mp34compfa on DNA
sequence libraries. This issue does not occur with the other
programs, which will recognize the appropriate sequence type, because
it is determined by the program (e.g. pv34compfx requires
DNA:protein).
Fixed substantial problem with 64-bit file offsets for Linux in
complib.c/comp_thr.c, p2_complib.c. This problem, solved by Doug
Blair, was preventing the threaded versions from working properly in
memory mapped mode.
In all earlier versions of fasta, when very long sequences were
searched, the sequence length reported was that of the "chunk" that
was actually searched (typically 80,000-query_length) rather than the
actual library sequence length. The peculiar behavior now changed,
and the full length of the library sequence, not the sequence chunk,
is reported as the library sequence length. Note that chunks are
still used, however, which can cause the same alignment to be shown
twice. In addition, the "-m 9" output format has changed to report
the coordinates of the query and library sequence (see below), which
may be different from 1-sequence_length because the the query and
library sequences may have been extracted from larger sequences. Four
additional fields have been added, "pn0", "px0","pn1", "px1" that are
the positions in for the beginning (pn0/1) and end (px0/1) of they
query/library sequence. pn0/1 would typically be changed with the
"@C:#" directive, described below.
Changes to doinit.c/initfa.c/initsw.c to provide a new function -
f_lastenv() - that allows function-specific adjustments to parameters
after the command line options have been read but before the first
sequence is read. This change solved problems with "mp/pv34compfx -S".
fasts34/tfasts34 now recognize that 'I/L' are the same, as are 'Q/K'
(which are apparently indistinguishable by Mass-Spec). The latter
identity is on by default, but can be turned off with "-h 0".
The MPI/PVM versions of the programs have been tested extensively with
compfa, compfx, and comptfx. Makefile.mpi4 now works properly.
Changes to p2complib.c to support the PVM option "-T 1-4", which
allows one to run on nodes 1-4 of a (presumably larger) PVM virtual
machine. This option has no effect on the mp34comp* programs. The
old "-T 4" to run on 4 nodes, is also available. If each node has 2
cpu's, as indicated in the "pvmd hostfile", both CPU's will be used
for a total, in this example, of 8 processes. This allows one to
specify a large PVM machine and use separate parts of it
independently.
Changes to nmgetlib.c to fix problems with longer dates in GCG files
(Y2K). Fixes to faatran.c for extended alphabets and 'X's. Various
code clean-ups to make "gcc -Wall" a little bit (not much) happier.
This is the first distributed fasta34 version.
================
>>Aug 9, 2001 CVS tag fa34t05
Corrections to initfa.c to allow -S to work with tfastx/y.
Fix to manshowbest.c for query position with -m 9.
>>July 18, 2001 CVS tag fa34t04
Various changes to complib.c, comp_thr.c, p2_complib.c, showbest.c,
showalign.c to deal with overlapping alignments in long sequences that
have been segmented. When long sequences are segmented (lcont>0), the
eventual total length (n1tot_v) is saved at beststr->n1tot_p. If
there was no lcont, then beststr->n1tot_p = NULL, and beststr->n1
should be used as the sequence length. This has the advantage of
requiring space only when long sequences are encountered, and
requiring only one integer for several segments.
m_msg.noshow has been removed.
The -m 9 format has been changed - 5 fields have been added, 4
(pmn0/pmx0/pmn1/pmx1) provide the beginning and end coordinates of the
query and library sequence; the last (fs) reports the number of
frameshifts. The names of the alignment boundaries have been changed
from min0/max0/min1/max1 to amn0/amx0/amn1/amx1 (Alignment miN/maX).
The SQL format has been extended to provide for statements that do
things but do not generate results, such as creating and selecting into a temporary table, e.g.:
================
do
create temporary table seq_pos (
id int unsigned not null auto_increment primary key,
prot_id int unsigned not null default 0,
start int unsigned not null default 0,
length int unsigned not null default 0,
)
;
do
insert into seq_pos (prot_id, start, length)
select id, 11, len-10
from protein, annot
where len > 100
and annot.protein_id = protein.id
and annot.pref=1
;
select seq_pos.id,
substring(protein.seq, start, length),
concat("@C:", start, " ", descr)
from protein, seq_pos, annot
where protein.id = annot.protein_id
and protein.id = seq_pos.prot_id
and annot.pref = 1
;
select prot_id,
concat("@C:", start, " ", descr)
from seq_pos, annot
where annot.protein_id = seq_pos.prot_id
and seq_pos.id = #
and annot.pref = 1
;
================
In the current implementation, these statements must start with "DO"
as the first two characters on the line, and come immediately after a
line ending with ';'. The text from "DO" to the next ";", excluding
the "DO", is executed when the database connection is made.
===== >>July 12, 2001
The allocation of the work_info data structure used to send
information to the worker threads has been changed. The old method
worked, possibly by accident.
A bug in p2_complib.c that caused E()-values to be calculated
improperly for the first query sequence has been fixed.
>>July 11, 2001 --> fa34t02
It is now possible to specify output coordinates in library sequences
by including the string: "@C:number" on the description line, e.g.
>gtm1_human gi|12345 human glutathione transferase M1 @C:21
would label the first residue in the library sequence "21" rather than
"1". This capability has been included to provide accurate
coordinates for searches done against subsequences generated by an SQL
query. For example, one could use a query of the form:
SELECT protein.id, substring(protein.seq,11,length(protein.seq)-20),
concat(protein.name," @C:11 ",protein.descr)
FROM protein;
to generate a sequence set with each sequence starting with residue
11. Without the "@C:11" option on the description line, the program
would number the alignment positions starting at 1, even though the
first residue of the sequence really started at 11. "@C:11" allows
one to correct the coordinate system.
Currently, "@C:offset" is available only with library type 1 (fasta
format) and 16 (mySQL).
The SQL-generated database with "@C:offset" can be used with both the
fast*34(_t) programs and with pv34comp*. However, the SQL syntax is
used differently in the fasta34 and pv34compfa programs. fast*34(_t)
requires three SQL statements during a search: (1) a statement to
generate a large set of library sequences; (2) a statement to generate
a description of a single sequence, given a unique identifier provided
by (1); and (3) a statement to generate a single sequence given a
unique identifier provided by (1). For fast*34 searches, the third
(3) SQL statement must provide the "@C:offset" information in the
third results field for the offset to be used. It is optional in (1)
and (2).
The pv34comp* programs only require one SQL statement, statement (1)
above, which must provide three fields, a unique identifier, the
sequence, and a complete description that must include "@C:offset" if
substrings are used. If SQL queries (2) and (3) are provided, they
are ignored. Thus, the same files can be used by both programs, but
the "@C:offset" is required in different SQL queries by the fast*34
and pv34comp* programs.
Other changes:
Re-incorporation of GAP_OPEN option; fix to Altschul-Gish stats when
GAP_OPEN is used.
Re-incorporation of A. Mackey's spam() improvement in dropnfa.
Fixes to include file ordering to allow fast*34(_t) pv34comp* programs
to compile.
Fix to lascii[] for SQL database queries.
Fix to an old bug in comp_thr.c to send individual worker_info
structures to threads (does not fix LINUX threads problems, however).
=====
>>July 9, 2001
Considerable changes to support no-global library functions.
(1) Separate ascii/sequence mapping arrays are used by the
query-reading (qascii), library-reading (lascii), and sequence
comparison function (pascii) routines. As a result, there is no
longer a need for tgetlib.o/lgetlib.o - lgetlib.o can serve both
functions.
(2) This also allows us to remove all #ifdef TFAST/FASTX conditionals
from complib.c/comp_thr.c/p2_complib.c. We no longer need
tcomp_thr.o, comp_thrx.o, etc. We still have a variety of
p2_complib.o variations to support the different c34.work* files.
(3) Because non-global openlib/getlib functions are available, exactly
the same open/get functions are available for reading both the
query and reference libraries in pv34comp* programs. The
host-specific openlib/getlib functions in hxgetaa.c are now
provided by nmgetlib.c, etc. This has two effect:
(a) it is now possible to compare a query database generated by an
SQL query to a library database generated by a different SQL
query.
(b) pv34comp* has lost (at least in this version) the ability to
automatically detect the query sequence type. To search with a
DNA query, you MUST use "-n".
(4) the resetp() function is now responsible for almost all of the
function sepcific (TFAST/FASTX/etc) initializations. All of the
function specific code has been removed from complib.c/comp_thr.c
and most of it has been moved to initfa.c/resetp().
(5) manageacc.c has been merged into compacc.c (mostly prhist()).
=====
>>June 1, 2001
Many changes to accommodate a new - no global variable - strategy for
reading sequence databases. Every time a file is opened, a struct
lmf_str is allocated which can be used for memory mapped files, ncbl2,
files, and mysql files.
In addition, an open'ed file has a default sequence type: DNA or
protein, or one can open a file in a mode that will allow the sequence
type to be changed.
=====
>>May 18, 2001 CVS: fa33t09d0
A new compile time parameter - -DGAP_OPEN, is available to change the
definition of the "-f gap-open" parameter from the penalty for the
first residue in a gap to a true gap-open penalty, as is used in BLAST
and many other comparison algorithms. This will probably become the
default for fasta in version 3.4.
Fixes to conflicts between "-S" and "-s matrix". When a scoring
matrix file was specified, lower-case alignments were not displayed
with -S (although the scores were calculated properly).
More extensive testting of mysql_lib.c (mySQL query-libraries) with
the pv4comp* and mp4comp* programs.
=====
>>April 5, 2001 CVS: fa33t08d4b3
Changes in nmgetlib.c and ncbl2_mlib.c to return long sequence
descriptions for PCOMPLIB (pv4/mp3comp*). Also fix p2_complib.c to
request DNA library for translated comparisons.
Fix for prss33(_t) to read both sequences from stdin.
=====
>>March 27, 2001 CVS: fa33t08d4
Modifications to allow 64-bit fseek/ftell on machines like Sun,
Linux/Intel, that support -D_FILE_OFFSET_BITS=64, -D_LARGE_FILE_SOURCE
off_t, and fseeko(), ftello() with the option -DUSE_FSEEKO. Machines
with 64-bit long's do not need this option. Machines with 32-bit
longs that allow files >2 Gb can do so with 64-bit file access
functions, including fseeko() and ftello(), which work with off_t file
offsets instead of long's.
=====
>>March 3, 2001 CVS: fa33t08d2
Corrected problems in nmgetaa.c and mysql_lib.c with parallel
programs, and one serious problem with alternate DNA scoring matrices
(initfa.c, initsw.c) not being set properly. A subtle problem with
the merge of scaleswn.c and scaleswg.c is fixed.
>>February 17, 2001
Modified mysql_lib.c to use "#", rather than "%ld", to indicate the
position of the GID. This change was made because sprintf() cannot be
used reliably to generate an SQL string, as '"' and '%' are used in
such strings.
=====
>>January 17, 2001
(no version change, date change)
Minor fixes to initfa.c, initsw.c to deal with DNA scoring matrices
properly. "-n -s dna.mat" is required for the sequence/matrix to be
recognized as DNA.
>>January 16, 2001
-->v34t00
Merge of the main CVS trunk - fa33t06 with the latest release branch,
fa33t08.
In addition, PCOMPLIB mods have been made to mysql_lib.c. Because
p2_complib.c gets sequence description information during the first
read of the database, the mysql_query must be changed to return:
result[0]=GID, result[1]=description, result[2]=sequence. In the
PCOMPLIB case, the other SQL queries (for GID description, sequence)
are not necessary but must still be provided.
./fasta-36.3.8h/doc/readme.v35 0000644 0001054 0001054 00000046607 13525131122 013232 0 ustar wrp
$Id: readme.v35 120 2010-01-31 19:42:09Z wrp $
$Revision: 55 $
>>Sep. 10, 2008
Fix problem in init_ascii() call for p2_complib2.c.
>>Sep. 9, 2008
Fix bug in display of library name when written to an output file
(rather than stdout).
>>Aug. 28, 2008 fa35_04_02 SVN Revision: 45
Fix serious bug in alignment generation that only occurred when large
libraries were used as a query with [t]fast[x/y]. This bug often
resulted in a core dump.
Address some other issues with uninitialized variables with -m 9c.
>>Jul. 15, 2008 fa35_04_01 SVN Revision: 38
Correct problems with Makefiles. Add information on compiling to README.
Address issue with mp_KS for -m 10 when searching small libraries.
>>Jul. 7, 2008 fa35_04_01 SVN Revision: 35
Fix problems that occurred when statistics are disabled with -z -1,
both for a normal library search, and for searches of a small library.
>>Jul. 3, 2008 SVN Revision: 33
Continue to fix an issue with 'J' and -S.
>>Jun. 29, 2008 SVN Revision: 29, 31
Fix additional problems with Makefiles, some issues uncovered with
Solars 'C' compiler (Rev. 30).
Discover serious bug when searching long, overlapping sequences, such
as genomes. The length of the library sequence was not updated to
reflect the length of the new region plus the overlap.
Fix inconsistency in the value of 'J' between uascii.h/aascii[] and
pascii[]. Add code to ensure that lascii[], qascii[], never return a
value outside pam2[][] (all <= pst.nsq) (particularly for 'O' and 'U'
amino-acids).
exit(0) returns for map_db, list_db.
>>Jun. 11, 2008
Correct bug in scaleswn.c that prevented exact matches to queries < 10
residues from being scored and displayed.
>>Jun. 1, 2008
Address various cosmetic issues in FASTA output:
(1) Modify comp_lib2.c so that -O outfile works when multiple queries are
compared in one run.
(2) remove the duplicated query sequence length in the 1>>>query line.
(3) in -m 10 output, the tags "pg_name" and "pg_ver" were duplicated, e.g.
>>>K1HUAG, 109 aa vs a library
; pg_name: fasta35_t
; pg_ver: 35.03
; pg_argv: fasta35_t -q -b 10 -d 5 -m 10 ../seq/prot_test.lseg a
; pg_name: FASTA
; pg_ver: 3.5 Sept 2006
The ; pg_ver and ; pg_name produced by the get_param() functions in
drop*.c have been renamed ; pg_ver_rel and ; pg_ver_alg.
>>>K1HUAG, 109 aa vs a library
; pg_name: fasta35_t
; pg_ver: 35.03
; pg_argv: fasta35_t -q -b 10 -d 5 -m 10 ../seq/prot_test.lseg a
; pg_name_alg: FASTA
; pg_ver_rel: 3.5 Sept 2006
Modify mshowbest.c, mshowalign.c to highlight E() values ( in HTML output.
>>Apr. 16, 2008 fa35_03_07
Merge fa35_ann1_br, which allows annotations in library sequences.
The PVM/MPI parallel version now support query sequence annotations
and -m 9c annotation encoding. It does not yet support library
annotations. Tested with both PVM and MPI.
>>Apr. 2, 2008 fa35_03_06
Ensure that code in last_init() to modify ktup never increases ktup value.
Add fasta_versions.html to more explicitly describe programs available.
>>Mar. 4, 2008
Fix parsing of parameters (matrix, gap open, gap ext) in ASN.1 PSSM
files produced by blastpgp.
>>Feb. 18, 2008 fa35_03_05
Re-implement -M low-high sequence range options. Sequence range
restriction has probably been missing since the introduction of
ggsearch and glsearch, which use a new approach to limiting the
sequence range.
>>Feb. 7, 2008 fa35_ann1_br
Add annotations to library sequences (they were already available in
query sequences). Currently, annotations are only available within
sequences, but they should be available in FASTA format, or any of the
other ascii text formats (EMBL/Swissprot, Genbank, PIR/GCG). If
annotations are present in a library and the annotation characters
includes '*', then the -V '*' option MUST be used. However, special
characters other than '*' are ignored, so annotations of '@', '%', or
'@' should be transparent.
In translated sequence comparisons, annotations are only available for
the protein sequence.
The format for encoded annotations has changed to support annotations
in both the query and library sequence. If the -m 9c flag is provided
and annotations are present, then an annotated position in the
alignment will be encoded as:
'|'q-pos':'l-pos':'q-symbol'l-symbol':'match-symbol'q-residue'l-residue'
For example:
|7:7:@@:=YY|14:14:##:=TT
In cases where the query or library sequence does not have an
annotation, then the q-symbol or l-symbol will be 'X' (which is not a
valid annotion symbol).
>>Jan. 25, 2008 fa35_03_04
Map 'O' (pyrrolysine) to 'K', 'U' (seleno-cysteine) to 'C' in uascii.h
('J' is already recognized and mapped to the average of 'I' and 'L').
Thus, 'J' will appear in alignments, but 'O' and 'U' are transformed
to 'K' and 'C'.
Because "Oo" and "Uo" are not (currently) part of aax[] ("Uu" is in
ntx[]), apam.c/build_xascii() was extended to add characters from
othx[] - "oth" for "other" so that they are not lost.
Double check, and fix, some mappings for 'J/j' and 'Z/z'.
>>Jan. 11, 2008 fa35_03_03
Clean up some issues with -m 10 output; put "; mp_Algorithm", ";
mp_Parameters" down with other -m 10 ";" lines. Also provide ";
al_code" and "; al_code_ann" if -m 9c is specified. Remove duplicate
">>>query" line.
Add "; aln_code" and "; ann_code" to -m 10 -m 9c output. The
alignment/annotation encoding is only produced once (in showbest(),
and is then saved for -m 10 aligment.
>>Dec. 13, 2007 fa35_03_02m (merge of fa35_03_02 and fa35_02_08_br)
Add ability to search a subset of a library using a file name and a
list of accession/gi numbers. This version introduces a new filetype,
10, which consists of a first line with a target filename, format, and
accession number format-type, and optionally the accession number
format in the database, followed by a list of accession numbers. For
example:
gi|1170095|sp|P46419|GSTM1_DERPT Glutathione S-transferase (GST class-mu)
The offset is 4 and the termination character is '|'. For databases
distributed in FASTA format from the European Bioinformatics
Institute, the offset depends on the name of the database, e.g.
>SW:104K_THEAN Q4U9M9 104 kDa microneme/rhoptry antigen precursor (p104).
and the delimiter is ' ' (space, the default).
Accession formats 1 and 3 expect strings; accession formats 2 and 4
work with integers (e.g. gi numbers).
>>Dec. 12, 2007 fa35_02_08
Correct bug in ssearch35 gapped scores that only occurred in
non-accelerated code. This bug has been present since fa35_02_06.
Modified the Makefiles so that accelerated (ssearch35(_t)) and
non-accelerated (ssearch35s(_t)) are available. Edited Makefile's to
provide accelerated ssearch35 more specifically.
Modifications to provide information about annotated residues in the
-m9c coded output. Previously, -m 9c output added a field:
=26+9=15-2=9-1=3+1=74-2=3-3=63
after the standard -m 9 output information. With the new version, an
annotated query sequence ( -V '*#' ) adds the field:
|14:16:#TA|44:37:*>ST|71:66:#=TT
which indicates that residue 14 in the query sequence aligns with
residue 16 in the target (library) with annotation symbol '#', the
alignment score is '<' less than zero, and the residues are 'T'
(query) and 'M' (library). (The '|' is used to separate each
annotation entry.)
>>Nov. 10, 2007
Parts of p2_complib.c and p2_workcomp.c, and the pvm/mpi Makefiles,
have been updated to be consistent with name changes in the param.h
and structs.h directories.
>>Nov. 20, 2007 fa35_02_08
Parts of p2_complib.c and p2_workcomp.c, and the pvm/mpi Makefiles,
have been updated to be consistent with name changes in the param.h
and structs.h directories.
>>Nov. 6, 2007 fa35_02_07
Correct problems with asymmetric RNA matrices in initfa.c and rna.mat.
>>Oct. 18, 2007
Correct problem parsing ASN1 FastaDefLines when the database is local.
Recovering from a misplaced cvs commit of code that was supposed to be
on a branch, code has been recovered from earlier versions (fa35_02_05
because fa35_02_06 has some branch contamination).
>>Oct. 4, 2007 fa35_02_06
Correct error in gap penalties in dropnnw.c. Due to an unfortunate
inconsistency, the gap parameter in FLOCAL_ALIGN (in dropgsw2.c) had a
different meaning than that in almost all the other programs (it was
the sum of gap_open and gap_ext). The FLOCAL_ALIGN function call was
copied for FGLOBAL_ALIGN, even though the the FGLOBAL_ALIGN function
used the more conventional gap_open, gap_ext parameters. Thus,
FGLOBAL_ALIGN was wrong and the subsequent do_walign() in dropnnw.c
were wrong. dropgsw2.c:FLOCAL_ALIGN has been modified to use the
conventional gap_open parameter, and calls to dropnnw.c:
FGLOBAL_ALIGN() and do_walign() have been fixed.
>>Sept. 20, 2007
Modify the logic used when saving a seq_record *seq_p into beststr
*bbp to ensure that if the seq_record is replaced, it is replaced at
all the places where it is referenced. This involves adding a linked
list into beststr (*bbp->bbp_link). When making the link (and freeing
it up), be certain that the linked seq_p is the same as the one being
replaced.
>>Sept. 18, 2007 fa35_02_05
A relatively obscure problem was found on the SGI platform when
searching a library smaller than 500 sequences (thus requiring some
shuffles). Two bugs were found and corrected; one involved not
allocating aa1shuff with COMP_THR and not do a m_file_p->ranliba()
before re_getlib(). The second involved destroying a pointer to the
list of seq_records when a sequence was being shuffled. The bugs were
confirmed with Insure, and have been fixed.
>>Sept. 7, 2007 fa35_02_04
Revamp the offset handling code to provide better uniformity between
query and library offsets and coordinate systems.
Fix a problem with load_mmap() to load 64-bit sequence locations
properly on machines with 32-bit integers.
>>Sept. 4, 2007
Modify ncbl2_mlib.c slightly to check to see whether the amino-acid
mapping in blast databases is identical to the FASTA mapping (it
should be). If they are identical, do not re-map the blast amino acid
sequences (potentially a small speed up).
>>Aug. 22, 2007
Change ps_lav.c to lav2ps.c, and add lav2svg.c. It is now possible to
generate a lalign35 HTML output that has both SVG (lav2svg) and PNG
(lav2ps | gs ), graphics.
>>Aug. 10, 2007 CVS fa35_02_03
Fix faatran.c:aacmap() bug.
>>Aug. 6, 2007
Extensive restructuring of pssm_asn_subs.c to parse PSSM:2 ASN.1's
downloaded from NCBI WWW PSI-BLAST more robustly.
>>July 25, 2007 CVS fa35_02_02
Change default gap penalties for OPTIMA5 matrix to -20/-2 from -24/-4.
>>July 24, 2007
Correct bugs introduced by adding 'J' - 'J' was initially put before
'X' and '*' in the alphabet, which led to problems because the
one-dimensional lower-triangular pam[] matrices (abl50[], abl62[],
etc) had entries for 'X', and '*', but not for 'J'. By placing 'J'
after the other characters, the problem is resolved.
Modify tatstats.c to accommodate 'J'.
'*' is back in the aascii[] matrix, so that it is present by default
(like fasta34).
>>July 23, 2007
Changes to support sub-sequence ranges for "library" sequences -
necessary for fully functional prss (ssearch35) and lalign35. For all
programs, it is now possible to specify a subset of both the query and
the library, e.g.
lalign35 -q mchu.aa:1-74 mchu.aa:75-148
Note, however, that the subset range applied to the library will be
applied to every sequence in the library - not just the first - and
that the same subset range is applied to each sequence. This probably
makes sense only if the library contains a single sequence (this is
also true for the query file).
Correct bugs in the functions that produce lav output from lalign35 -m
11 to properly report the begin and end coordinates of both sequences.
Previously, coordinates always began with "1". Correct associated bug
in ps_lav.c that assumed coordinates started with "1".
>>June 29, 2007 CVS fa35_02_01
Merge of HEAD with fasta35 branch.
>>June 29, 2007 CVS fa35_01_06
Add exit(0); to ps_lav.c for 0 return code.
>>June 26, 2007
Add amino-acid 'J' for 'I' or 'L'.
Add Mueller and Vingron (2000) J. Comp. Biol. 7:761-776 VT160 matrix,
"-s VT160", and OPTIMA_5 (Kann et al. (2000) Proteins 41:498-503).
Changes to dropnnw.c documentation functions to remove #ifdef's from
strncpy() - which apparently is a macro in some versions of gcc.
>>June 7, 2007
Modify initfa.c to allow ggssearch35(_t), glsearch35(_t) to use PSSMs.
>>June 5, 2007 CVS fa35_01_05
Modifications to p2_complib.c, p2_workcomp.c to support Intel C
compiler. Fixed bug in p2_workcomp.c - gstring[2][MAX_STR] required -
[MAX_SSTR] too short. mp35comp* programs now tested and working (as
are pv35comp*, c35.work* programs).
Fix problem with fasts/fastm/fastf last_tat.c with limited memory.
Correct problem with lalign35.exe Makefile.nm_[fp]com.
Add $(CFLAGS) to map_db to enable large file support.
Address problem with PSSM's when '*' not defined (initfa.c:extend_pssm()).
>>May 30, 2007 CVS fa35_01_04
Complete work on ps_lav, which converts an lalign35 lav (-m 11) file
into a postscript plot, which looks identical to the plots produced by
plalign from fasta2. (ps_lav has been replaced by lav2ps and lav2svg).
>>May 25,29, 2007
Changes to defs.h, doinit.c mshowalign.c for -m 11, which produces lav
output only for lalign35.
Changes to comp_lib2.c to add m_msg.std_output, which provides all the
standard print lines. This is turned off for -m 11 (lav) output.
lalign35 -m 11 provides standard lav output, with the addition of
#lalign35 -q ... .
>>May 18, 2007
Add m_msg.zsflag to preserve pst.zsflag when reset by global/global
exclusion of many library sequences.
>>May 9, 2007 CVS fa35_01_03
Tested local database size determination with p2_complib2/p2_workcomp2.
>>May 2, 2007 renamed fasta35, pv35comp, etc
Separate thread buffer structures from param.h.
Problems with incorrect alignments has been fixed by re-initializing the
best_seqs and lib_buf2_list.buf2 structures after each query sequence.
The labels on the alignment scores are much more informative (and more
diverse). In the past, alignment scores looked like:
>>gi|121716|sp|P10649|GSTM1_MOUSE Glutathione S-transfer (218 aa)
s-w opt: 1497 Z-score: 1857.5 bits: 350.8 E(): 8.3e-97
Smith-Waterman score: 1497; 100.0% identity (100.0% similar) in 218 aa overlap (1-218:1-218)
^^^^^^^^^^^^^^
where the highlighted text was either: "Smith-Waterman" or "banded
Smith-Waterman". In fact, scores were calculated in other ways,
including global/local for fasts and fastf. With the addition of
ggsearch35, glsearch35, and lalign35, there are many more ways to
calculate alignments: "Smith-Waterman" (ssearch and protein fasta),
"banded Smith-Waterman" (DNA fasta), "Waterman-Eggert",
"trans. Smith-Waterman", "global/local", "trans. global/local",
"global/global (N-W)". The last option is a global global alignment,
but with the affine gap penalties used in the Smith-Waterman
algorithm.
>>April 24, 2007
The new program structure has been migrated to the PVM and MPI
versions. In addition, the new global algorithms (pv35compgg,
pv35compgl) have been moved, though the the PVM/MPI versions do not
(yet) to the appropriate size filtering.
>>April 19, 2007
Two new programs, ggsearch35(_t) and glsearch35_t are now available.
ggsearch35(_t) calculates an alignment score that is global in the
query and global in the library; glsearch35_t calculates an alignment
that is global in the query and local, while local in the library
sequence. The latter program is designed for global alignments to domains.
Both programs assume that scores are normally distributed. This
appears to be an excellent approximation for ggsearch35 scores, but
the distribution is somewhat skewed for global/local (glsearch)
scores. ggsearch35(_t) only compares the query to library sequences
that are beween 80% and 125% of the length of the query; glsearch
limits comparisons to library sequences that are longer than 80% of
the query. Initial results suggest that there is relatively little
length dependence of scores over this range (scores go down
dramatically outside these ranges).
A bug was found and fixed in showalign() and showbest() where the
aa1save buffer was not preserved when some sequences needed to be
re-read, while others were stored in the beststr.
>>April 9, 2007
Some of the drop*.c functions have been reconfigured to reduce the
amount of duplicate code. For example, dropgsw.c, dropnsw.c, and
dropnfa.c all used exactly the same code to produce global alignments
(NW_ALIGN() and nw_align()), this code is now in wm_align.c.
Likewise, those same files, as well as dropgw2.c, use identical code
to produce consensus alignments (calcons(), calcons_a(), calc_id(),
calc_code()). Rather than working with three or four copies of
identical code, there is now one version.
>>March 29, 2007
At last, the lalign (SIM) algorithm has been moved from FASTA21 to
FASTA35. Currently, only lalign35 is available. A plotting version
will be available shortly (or perhaps a more general solution that
produces lav output).
The statistical estimates for lalign35 should be much more accurate
than those from the earlier lalign, because lambda and K are estimated
from shuffles.
Many functions have been modified to reduce the number of times
structures are passed as arguments, rather than pointers.
>>February 23, 2007
The threading strategy has been modified slightly to separate the end
of the search phase (and a complete reading of all results buffers)
from the termination phase. This will allow future threading of
subsequent phases, including the Smith-Waterman alignments in
showbest() and showalign() (though care will be required to ensure
that the results are presented in the correct order).
>>February 20, 2007 fasta-34_27_0 (released as fasta-35_1)
The FASTA programs have been restructured to reduce the differences
between the threaded and unthreaded versions (and ultimately the
parallel versions) and to make more efficient use of modern large
memory systems. This is the beginning of a move towards a more robust
shuffling strategy when searching databases with modest numbers of
related sequences.
The major changes:
comp_lib.c -> comp_lib2.c - comp_lib.c will be removed
work_thr.c -> work_thr2.c - work_thr.c will be removed
mshowbest.c, mshowalign.c have been modified to remove aa1 as an
argument. They must allocate that space if they need it.
The system is set up to allocate a substantial amount of library
sequence memory, either to a single buffer (unthreaded) or to the
threaded buffer pool. For smaller databases, the library sequences
are read once, and then subsequently read from memory (this could be
extended for RANLIB(bline) as well).
Soon, these changes will allow the program to re-read the beststr[]
sequences and shuffle them to produce accurate lambda/K estimates.
================================================================
See readme.v34t0 for earlier changes.
================================================================
./fasta-36.3.8h/doc/readme.v36 0000644 0001054 0001054 00000303604 13525131122 013224 0 ustar wrp
Version 3.6 of the FASTA programs is a significant update over version
3.5. It uses the same underlying structure as FASTA35 (specifically
the strategies for ensuring accurate statistics), but it allows for
multiple high-scoring alignments to be shown, rather than just one.
This is the main functional difference between FASTA and BLAST -
BLAST could show multiple HSPs, FASTA did not.
>>Aug. 9, 2019
[src/ncbl2_mlib.c, ncbl2_head.h]
Modest extensions made to support reading makeblastdb format v5
databases. Changes have only been made to read the db.pin file, but
things work in simple tests.
>July 16, 2019
[src/comp_lib9.c]
Fixed a memory leak problem when searching with large libraries that
could be memory mapped (libraries with .xin index files). If the
library did not fit in memory, then the kept allocating new memory.
By default, the largest database that fits in memory must be less than
16 GB. Larger libraries will be re-read, which slows down multi-query
searches considerably. To increase the size of the library allowed in
memory, use the option: "-X M32G" to fit 32 GB libraries.
>>Mar. 8, 2019
[src/initfa.c,faatran.c,dropfx2.c]
Modify translation table 1 to allow selenocysteine translation
(TGA->'U'), and modify scoring matrices to give positive scores to
'*':'U'. The translation modification ONLY works with "-t 1". In
addition, BLAST BTOP alignments (-m 8CB) convert a 'U' aligned with a
'*' to a '*', so the end of the alignment is '**' rather than 'U*'
(fastx36) or '*U' (tfastx36).
dropfx2.c (fastx36/tfastx36), dropfz3.c(fasty36/tfasty36) did not
properly switch protein and translated DNA codes with -m 8CB -- fixed.
version date updated to Mar, 2019
>>Feb. 26, 2019
[scripts/get_genome_seq.py]
added get_genome_seq.py as a replacement for get_hg38_bed.py, remove
get_hg38_bed.py. 'get_genome_seq.py --genome mm10' also produces
sequences from mouse mm10 (and can now do any genome that bedtools can
read).
>>Feb. 23, 2019
[src/comp_lib9.c, mshowbest.c]
Modify repeat_thresh so that poor alignment scores (E() >
ppst->e_cut_r, typically -E-threshold/10.0) do not look for additional
alignments.
>>Feb. 21, 2019
[src/nmgetaa.c, scaleswn.c, scripts/get_protein.py, get_hg38_bed.py]
Modify nmgetaa.c to ignore ':'s (for sequence subsets) in scripts.
The script can do the subsetting. Modify scripts/get_protein.py to
provide subsetting. Add scripts/get_hg38_bed.py to extract fasta
sequences using the format "chr2:123456-543210"
Modify scaleswn.c to estimate Altshul-Gish parameters when gap and
extension do not match exactly.
>>Feb. 6, 2019
[src/compacc2e.c, nmgetaa.c]
modify build_link_data() to allow '+' for space in scripts. Ensure
that lib_type is properly initialized (open_lib.c()).
>>Jan. 23, 2019
[nmgetaa.c]
Fix bug introduced when checking for lib_type.
>>Jan. 15, 2019
[src/upam.h, altlib.h, nmgetaa.c]
[scripts/rename_exons.py, map_exons_coords.py, get_uniprot.py, get_refseq.py, get_proteins.py]
Bug fixes: The VT10, VT20, etc scoring matrices did not have scores for '*:*'
alignments, used with FASTX/TFASTX for extending alignments through
the termination codon. As a result, searchs with '-t t' did not
extend through the termination codon, even though they should have.
This has been fixed.
Enhancements: FASTA can now download both query and library sequences using a script, by specifying file type 9. Thus:
fasta36 "../scripts/get_uniprot.py+P09488 9" /seqlib/swissprot.fasta
Will run the script "get_uniprot.py" with the argument "P09488" and
use the output of the script as the query sequence. In this example,
the library type (9) is specified by the " 9" (this space cannot be
replaced with a '+' character).
Alternatively, library type '9' can be specified by putting a '!' before the script file name.
fasta36 \!../scripts/get_uniprot.py+P09488 /seqlib/swissprot.fasta
Scripts can be used to produce query or library sequences, or both.
Three scripts that download sequences from the NCBI and Uniprot have
been added in the "scripts" directory: "get_uniprot.py" takes Uniprot
accessions as arguments, "get_refseq.py" takes refseq accessions
(protein or mRNA), and "get_protein.py" gets both Uniprot and RefSeq
protein sequences.
rename_exons.py and map_exons_coords.py can take annotated BTOP
alignments with genome coordinates and map exons to the alternative
genome.
>>Jan. 2, 2019
[src/mshowbest.c]
Fix problems with site annotation when dom_info is provided with -m8CBL
[scripts/ann_exons_up_sql.pl, ann_exons_up_www.pl]
Make scripts more robust to missing chromosome information,
reverse-strand coordinates.
>>Dec. 11, 2018
[scripts/ann_exons_up_www.pl, ann_exons_up_sql.pl]
Add the option "--gen_coord" to report exon start ('<') and end ('>')
genome coordinates features of exons.
>>Nov. 14, 2018
[scripts/rename_exons.py, relabel_domains.py, compacc2e.c]
Two new scripts, rename_exons.py and relabel_domains.py, that take a
blast tabular output file with domain alignment annotations (and
possibly raw domain information) and modifies the names
(rename_exons.py) or colors (relabel_domains.py). rename_exons.py
takes the exon numbering associated with the query sequence and maps
it onto the subject alignments. relabel_domains.py can be used to use
different color numbers for homologous and non-homologous domains.
Both of these programs modify blast tabular output files, which can
then be merged back into an alignment display using
merge_blastp_annot.pl or merge_fasta_annot.pl.
compacc2.c:build_link_data() has been modified to convert '+' in the
script string to ' ', to allow passing command line options. A space
in the script string is used to separate the script from the library
type of the file returned by the script.
>>Nov. 6-7, 2018
[doinit.c, mshowbest.c, mshowalign2.c, defs.h, structs.h]
(a) Add options to provide query and subject sequence lengths and raw
domain coordinates in BLASTP tabular output with the options -m 8CBl
and -m 8CBL. If domain annotations are available, -m 8CBL also
provides the raw domain coordinates (not just those included in the
alignment) in the form |DX:1-100;C=PF12345|XD:1-100;C=PF12345 where
|DX a query annotation and |XD indicates a subject annotation. -m
8CBl (lower-case L) shows the sequence lengths, but not the raw domain
info.
(b) parse the annotation program strings so that '+' are converted to
' '. This greatly simplifies passing arguments to the annotation scripts. Thus:
-V \!ann_pfam_sql.pl --db=pfam31 --neg --vdoms can be written as:
-V \!ann_pfam_sql.pl+--db=pfam31+--neg+--vdoms (likewise for -V q\!ann_pfam...)
(c) provide an option to remove region/feature annotations from non-m8
(blast-tabular) output. This simplifies the process of using
scripts/merge_fasta_btab.pl to use .bl_tab (-m 8CBL) files to inject
sub-alignment scores and domain information.
>>Nov. 1, 2018
[doinit.c]
Allow -m F#=file.name in addition to -m "F# file.name" to address
problems I had with spaces in shell scripts.
>>Oct. 23, 2018 [re-released as fasta-36.3.8g] (see README_v36.3.8g.md)
[make/Makefiles*,psisearch2/m89_btop_msa2.pl]
Add options to psisearch2/m89_btop_msa2.pl to provide clustalw header
(--clustal), require a minimum coverage of the query sequence
(--min_align 0.8), and edit sequence identifiers to remove database
and accession (--trunc_acc).
Remove -lz dependency from non-debug Makefiles.
>>Aug. 5, 2018 [re-released as fasta-36.3.8g]
[lib_sel.c]
Make lib_select.c more robust to missing indirect name files.
[scripts/ann*.pl]
update various annotation scripts to use https:// instead of http://
>>April 3, 2018
[initfa.c, comp_lib.c, dropfx2.c]
Changes to (a) ensure that the "-t t" option correctly inserts and
aligns a termination codon '*'. (a) changes to -m 8CB, -m8CC, and -m9C
so that aligned termination codons are indicated as "**" (-m8CB) or
"*1" (-m8CC, -m9C).
>>Mar. 9, 2018
[scripts/annot_blast_btop2.pl, merge_blast_btab.pl, blastp_annot_cmd.sh]
Code is now in place to provide sub-alignment scoring using domain
annotations with blastp searches (BLOSUM62 only). blastp_annot_cmd.sh
runs blast and produces both a standard HTML and a tabular output
file. It then runs annot_blast_btop2.pl to add sub-alignment scoring
to the tabular ouput file, and then merge_blast_btab.pl merges the
domain-annotated blast tabular file with the HTML output file. When
combined in this way, the FASTA web server (fasta.bioch.virginia.edu)
can produce blastp searches with domain highlights/scoring.
>>Feb. 6, 2018
[initfa.c, doinit.c, mshowbest.c, mshowalign2.c]
Add a new extended option, -XB, which causes percent identity, percent
similarity, and alignment length to be presented using the BLAST
model, which does not count gaps in the alignment length.
>>Dec. 30, 2017 [released as fasta-36.3.8g]
[scaleswn.c]
Replace np_to_z() with np1_to_z(), which does not substract low
probability from 1.0, thus allowing accurate z-values for very low
probabilities.
>>Sept. 26, 2017
[comp_lib9.c, compacc2e.c]
Previously, if the query sequence was all lower-case letters (seg-ed)
and the '-S' option specified, the search would effectively be done
with a zero-length sequence, which broke the statistics. The code has
been modified to convert all lower-case queries to upper-case when -S
is used.
[scaleswn.c]
Fixed problem with scaleswn.c/ag_stats() not setting parameters
properly when matrix was unknown.
>>May 23, 2017 [released as fasta-36.3.8f]
[url_subs.c]
A small, but major change in the output available to the $SRCH_URL and
$SRCH_URL2 strings, which are used to enable re-searching, and now
pairwise alignment. (It would be better to provide a json string of
the information, rather than using fprintf().) An additional value,
the name of the query sequence, is provided to these urls so that
pairwise alignment becomes possible.
>>May 23, 2017
[scripts/ann_feats2ipr.pl,ann_feats_up_www2.pl,test_ann_scripts.sh src/defs.h]
Changes to ensure that EBI format databases, which place the ID before
the accession, e.g. SP:GSTM1_HUMAN P09488, can be processed properly
by annotation scripts. This involved displaying more of the
description line, so that the accession field is included, in the
annot_XXXXX file.
>>May 8, 2017
[compacc2e.c]
Address problem where initial domain annotation similarity
score/identity not properly reset.
[scripts/annot_blast_btop2.pl]
Fix various problems with domain scores, particularly in gaps, and
domain coordinates.
Modify version string to May, 2017
>>April 18, 2017
[cal_cons2.c]
Address problem where identity count not correctly assigned to
N-terminal domain at the end of a domain.
>>April 14, 2017
[src/compacc2e.c, scripts/ann_exons_up_www.pl]
Provide a new script to annotate exon positions in Uniprot Proteins
(scripts/ann_exons_up_www.pl) that uses the EBI proteins/api/coordinate service.
Provide additional error checking on annotates to ensure that domain
start is always <= domain end.
>>Jan 17, 2017
[scripts/ann_pfam30_tmptbl.pl]
ann_pfam30_tmptbl.pl is a modification of ann_pfam30.pl that loads a
temporary tables of accessions to be annotated, rather than asking for
one sequence at a time.
>>Dec 14, 2016
[initfa.c/scaleswn.c]
Change required shuffle count (down to 100) and introduce an
median/IQR strategy to robustly estimate mean and S.D. for ggsearch
(normal) comparisons (-z 3, in place of Altschul-Gish statistics).
Modify version string to Dec., 2016.
>>Nov 18, 2016
[build_ares.c]
fix sequence encoding memory leak
>>Sept 30, 2016 [released as fasta-36.3.8e]
[psisearch2/]
Added a new sub-directory, psisearch2/, which includes scripts and
documentation for the new iterative psisearch2_msa.pl and
psisearch2_msa.py programs. These programs perform iterative PSIBLAST
(or SSEARCH) searches, but with an option (--query_seed) that
dramatically reduces false-positives.
Modified most of the scripts/ann_*.pl files to work with new NCBI
Swissprot accession format. Modified scripts/ann_feats_up_www2.pl and
scripts/ann_upfeats_pfam_e.pl to work with JSON format Uniprot
descriptions.
>>July 28, 2016
[src/pssm_asn_subs.c]
Fix another problem with binary ASN.1 file processing where the
asnp->abp buffer was not refilled in time.
>>July 12, 2016
[src/mshowbest.c]
Modified -m8/-m 8CB output to include "eval2" when a second E()-value
is available (when -z > 20). "eval2" is shown after the bit score,
but before BTOP and annotations.
>>May 25, 2016
[scripts/ann_pfam28.pl]
Implement --split_over command option, which takes overlapping domains
and produces virtual like domains from the overlap region.
>>Apr. 12, 2016 [released as fasta-36.3.8d]
[src/pssm_asn_subs.c]
Fix another problem with binary ASN.1 file processing where the
asnp->abp buffer was not refilled in time.
[initfa.c] - version date updated to Apr, 2016
[upam.h] - changes to default gap penalties for VT40 (from -14/-2 to
-13/-1), VT80 (from -14/-2 to -11/-1), and VT120 (from -10/-1 to 11/-1).
>>Mar. 30, 2016
[scripts/m9B_btop_msa.pl]
Provide --bound_file_only, --bound_file_in, --bound_file_out.
Ensure that alignments outside boundaries are NOT included in MSA.
>>Mar. 22, 2016
[scripts/m8_btop_msa.pl, m9B_btop_msa.pl]
Ensure that full length query sequence is included in MSA.
[pssm_asn_subs.c]
Fixes to allow IUPACAA sequences in ASN.1 PSSM. Other fixes to ensure
that arrays not allocated are not freed when wfreqs2d[] is not available.
>>Mar. 18, 2016
[scripts/m8_btop_msa.pl, m9B_btop_msa.pl]
scripts/m8_btop_msa.pl takes a fasta36 -m 8CB output file and produces
a multiple sequence alignment that can be used with psi-blast.
scripts/m9B_btop_msa.pl takes a fasta36 -m 9B output file and produces
a multiple sequence alignment that can be used with psi-blast.
>>Feb. 15, 2016
[mshowbest.c, compacc2e.c, cal_cons2.c, dropfx2.c, dropfz3.c]
Modify logic for calculating percent identity in sub-alignments to use
the BLASTP strategy, which does not could gapped regions as part of
the alignment length. Fix the -m 8 display (BLAST tabular output) to
use ungapped alignment length for percent identity (as -m BB does).
[initfa.c] - version date updated to Feb, 2016
>>Feb. 12, 2016
[compacc2e.c, cal_cons2.c, dropfx2.c, dropfz3.c]
Modify display_push_features() to use both the rst.score[score_ix],
which is used to calculate the zscore and bitscore, and also sw_score,
which is the correct divisor for sub-alignment scores. Previously,
only the rst.score[score_ix] was used, which caused some bit scores to
be out of range, and produced erroneous Q-value scores for
sub-alignments.
>>Jan. 24, 2016
[cal_cons2.c]
Ensure left_domain_link[01] set to NULL before initialized.
Rename ann_feats2l.pl to ann_feats_up_sql.pl for consistency with
ann_feats_up_www2.pl. ann_feats_up_www2.pl no longer works because of
changes at the EBI.
>>Dec. 15, 2015 [re-released as fasta-36.3.8c]
[pssm_asn_subs.c]
Fixed another problem parsing ASN.1 because of reading past the end of
the buffer.
[cal_cons2.c]
Fix a serious bug that prevented display of annotated sites using -m9c/-m8CC
>>Nov. 24, 2015 [re-released as fasta-36.3.8c]
[mshowalign2.c]
Correct first_line logic to display >>seqid description on first
alignment line, but >- on remaining lines.
>>Nov. 23, 2015 [released as fasta-36.3.8c]
[cal_cons2.c, mshowalign2.c, scripts/annot_blast_btop.pl, scripts/ann*_e.pl]
Fix the problem that lalign36 no longer displayed the library/subject
accession/description. Correct some problems introduced with BTOP
alignment encoding.
A new script, scripts/annot_blast_btop.pl, is available to provide -V
type sub-alignment scoring to BLASTP BTOP alignments stored in tabular
files. In addition, the scripts/ann*.pl scripts were modified to work
as part of a unix pipe, and the ann*_e.pl scripts replace the older
non "_e.pl" scripts, and were renamed with out the "_e" (thus,
ann_pfam_www.pl was removed, and ann_pfam_www_e.pl was renamed
ann_pfam_www.pl).
>>Nov. 6, 2015
[cal_cons2.c, initfa.c, mshowbest.c, dropfx2.c, dropfz3.c]
Implement BLAST+ BTOP alignment format, available with -m 8CB or -m 9B.
Convert previously static calc_code alignment strings to dynamic strings.
>>Oct. 13, 2015 [released as fasta-36.3.8b]
[initfa.c, pssm_asn_subs.c]
Fix problems encountered when reading in binary ASN.1 file produced by
datatool. Previous versions did not use the final score data provided
by the tool; this version now uses that information if it is
available. If it is not available, the PSSM integer values are
calculated from the frequency data.
>>Oct. 8, 2015
[pssm_asn_subs.c]
Fix a rare condition where the pssm_asn parser reads past the asn
buffer.
>>Sep. 28, 2015
[comp_lib9.c, scaleswn.c, dropnfa.c, dropfx2.c dropfz3.c]
(1) [scaleswn.c] -- changes to drop back to Altschul-Gish statistics
when other strategies fail. (2) Fix to ensure that adler32() is
calculated correctly for 1-residue library sequences; definition of
adler32() added to drop*.c files.
>>Sep. 7, 2015
[Makefile.nmk_icl, Makefile.nm_pcomp, doinit.c, readme.win32]
Automatic detection of thread/core number on windows. Changes to
readme.w32 documentation, Windows programs no longer require sse2 in
name (since all modern x86 processors have it).
>>Sep. 4, 2015
[comp_lib9.c, cal_cons2.c, dropfx2.c, dropfz3.c]
(1) Fix bug with overlapping domains when a domain ends exactly where
the alignment starts. (2) provide command line in -m 8CC output with -DPGM_DOC
>>Aug. 31, 2015 [git v36.3.8_30Jul15]
[cal_cons2.c, dropfx2.c, dropfz3.c, mshowbest.c, build_ares.c, doinit.c, comp_lib9.c]
Modifications to enhance the independence of annotation output to
different files. Earlier, annotations could not be properly output to
different files in different formats. For example, -m 9c prevented -m
"F8CC output.m8CC" -m "F9I ouutput.m9I". Annotation output formats
are now more independent. They are not fully independent, however.
Thus, if CIGAR format is used for one output, it will be used in all
other alignment encoding outputs.
>>Aug. 21, 2015
[cal_cons.c, dropfx2.c, dropfz3.c, mshowbest.c, build_ares.c, doinit.c]
Add -m 9I to -m 9i. -m 9i reports identity and variation (based on
annotation scripts). -m 9I also reports domain content on the initial
summary line.
>>Aug. 20, 2015 [fasta-36.3.8a]
[mshowalign2.c]
Fixed bug in lalign36 E()-value, bit score calculations for highest
scoring non-identical alignment by reverting to older code. This bug
was introduced in fasta-36.3.6d in January, 2014.
>>Jul. 21, 2015 [fasta-36.3.8]
[compacc2e.c, cal_cons2.c, dropfx2.c dropfz3.c, param.h]
Fixed a major bug in the annotation code that had been added to
accomodate overlapping domains. The original implementation was not
thread-safe, because the array of annotations was modified during the
scoring, but was also shared by threads. The new version keeps
independent scoring arrays.
>>Jun. 23, 2015 [released as fasta-36.3.7b]
[dropnnw2.c]
Fix problem where glsearch reset (ignored) the -M sequence limit.
>>Jun. 18, 2015
[dropfx.c, dropgsw.c, dropfx.c, dropfx2.c, dropfz3.c]
Fix problem in do_walign.c with comparison to score_thresh during
recursive alignment.
>>May. 21, 2015
[compacc2e.c]
Add additional checks to ensure that annotations are within the
sequence boundaries.
>>Jan. 26, 2015 [ re-released as fasta-36.3.7a]
[compacc2e.c]
Fix problem with domain boundary calculations for subsets of sequences.
>>Jan. 21, 2015 [ released as fasta-36.3.7a]
[calc_cons2.c, dropfx2.c, dropfy3.c]
Fix problems with -m 9c / -m 9C alignment encodings in version
36.3.7. Apparently, the Nov. 25, 2014 fix was not committed properly.
In addition, make certain that the query sequence is ALWAYS the
reference sequence, particularly in translated alignments. As a
result, the insertion/deletion codes are now reversed for fast[xy]36
and tfast[xy]36.
>>Jan. 6, 2014
[data/VTML_*.mat]
Provided scoring matrix files for the VTML_10,20,40,80,120,160,200
matrices available internally.
>>Nov. 25, 2014 [ released as fasta-36.3.7]
[cal_cons.c, dropfx2.c, dropfz3.c]
Fix problem that prevented -m 9c and -m 8CC unless annotations were
present.
Added approved copyright notice and Apache 2.0 license to
appropriate files.
>>Nov. 19, 2014
[mshowbest.c]
Add alignment (CIGAR) string and annotation string to BLAST tabular
(-m 8) aligments with -m 8C[cCdD]. To get alignment and annotation
encoding without BLAST comments, use -m 8X[cCdD].
>>Nov. 10, 2014
[cal_cons2.c, dropfx2.c, dropfz3.c]
Ensure that site annotations are shown when annotations are embedded
in a sequence, not provided by a script.
>>Oct. 27, 2014
[cal_cons2.c]
Fix a bug in the annotation alignment that put annotation symbols off
by one (or more) in the coordinate lines. Add annotations that align
in gaps.
>>Oct. 6, 2014
[most source files]
The copyright notice for fasta-36.3.7 has been updated to include an
open software license, Apache2.0, for redistribution.
>>Sept. 28, 2014
[url_subs.c]
Substitute annot_p->s_annot_arr_p[] for annot_p->domain_arr_p[i] in
display_domains(), encode_json_str(). Remove domain_arr_p from struct
annot_entry. With domain_arr_p gone, n_domains is less useful, but it
is still available, and used for checking for domain graphics.
encode_json_domains() also now uses annot_p->n_annots, and skips over
non-domains.
>>Sept. 19, 2014
[dropfx2.c, dropfz3.c]
Fixes to produce correct coordinates with forward and reverse
complement [t]fast[x,y].
>>Sept. 17, 2014 [new version, fasta-36.3.7]
[compacc2e.c, cal_cons2.c, dropfx2.c, dropfz3.c]
The annotation domain scoring/plotting strategy has been extended to
allow overlapping domains. To accommodate overlapping domain
annotations, the annotation file format (e.g. gstm1_human.annot) has
been extended to accept the form:
>sp|P09388|GSTM1_HUMAN
1 - 88 Glutathione_S-Trfase_N :1
7 V F Mutagen: Reduces catalytic activity 100- fold.
90 - 208 Glutathione-S-Trfase_C-like :2
108 V Q Mutagen: Reduces catalytic activity by half.
where a "-" in the second field indicates that the first and third
fields specify the beginning and end of the domain. In previous
versions, a '[' specified the beginning of a domain, and a ']' on a
later line specified the end of the domain. '[' and ']' on separate
lines required that domains not overlap (so that the '[' and ']' could
be paired). fasta-36.3.7 will still read this format, but the "start -
stop" format is both simpler and more flexible.
Three new annotation scripts are available that use the new domain
notation: ann_feats2ipr_e.pl, ann_feats_up_www2_e.pl, ann_pfam_e.pl,
and ann_pfam_www_e.pl. All four scripts will report overlapping
domains.
Overlapping domains also allows domain annotations from different
sources to be combined (e.g. InterPro Pfam, Panther, and Superfamily
domain annotations), as well as domain annotations of different types,
e.g. Uniprot domain and secondary structure annotations.
>>Aug. 28, 2014 [re-released as fasta-36.3.6f]
[ncbl2_mlib.c]
The code used to parse blastfmtdb sequence description lines has not
kept up with NCBI's use of ASN.1 in sequence descriptions. This code
has been updated, and now works properly with the protein and DNA
sequence databases.
[comp_lib9.c]
Fixed a seg-fault that occurred when an open-file error occurred.
>>Aug. 22, 2014 [released as fasta-36.3.6f]
[mshowbest.c]
Change alignment summary display for lalign to not show identical
alignment score unless '-J' option used. Add "The best non-identical
alignments" when no "-J"
[ann_pfam_www.pl] Fix bugs.
[ncbl2_mlib.c]
modified to read NCBI ambiguity codes in
blastdbfmt/formatdb nucleotide databases. Not extensively tested.`
>>Aug. 20, 2014
[compacc2.c, cal_cons.c, dropfx.c, dropfz2.c]
Modify sub-alignment score report to calculate bit-score by dividing
total alignment bit score by sub-alignment raw score divided by total
alignment raw score. This produces a bit score that is much more
sensible than the previous strategy, which calculated a z-score from
the sub-alignment.
>>Aug. 18, 2014
[compacc2.c, cal_cons.c]
Undo removal of '[]' from aa0a/aa1a (they are required to visualize
domain boundaries in alignment). cal_cons.c now users PSSMs when they
are available.
>>Aug. 8, 2014
[comp_lib9.c, compacc2.c]
Move the call to get query annotations via scripts out of compacc2.c
and into comp_lib9.c.
>>July 29,2014
[comp_lib9.c, mshowbest.c, mshowalign2.c]
Enable high scoring alignment display (like high scoring sequences)
with lalign36, when -m 9 (-m 9c/d/C/D) option is provided, or with -m
8. This allows lalign36 to provide a compact, tabular list of
non-overlapping local alignments.
>>June 30, 2014
[pssm_asn_subs.c]
Update the code for parsing ASN.1 binary PSSM files produced by
psiblast+. The new code reads more of the optional fields in
pssm_intermediate_data(). The fields are not used, but broke the
earlier parser.
>>June 11, 2014
[cal_cons.c, initfa.c, dropfx.c, dropfz2.c]
Extend the match/mismatch encoding provided by -m 9c and -m 9C with -m
9d and -m 9D. The -m 9d/D options provide mismatch locations as well
as insertion/deletion locations. For -m 9d, the list of codes has
expanded from '=\/*' to '=\/*x'; for -m 9D, 'MDIMX'. Current
implementation works for all programs except [t]fast[fms]. Updated
version strings to June, 2014.
>>May 28, 2014
[mshowalign2.c, mshowbest.c, initfa.c, structs.h]
Add the command line option -XI. Changes the calculation of percent
identity to ensure that a single mismatch in a long sequence with >
99.9\% identity is displayed as 99.9% (0.999) identity, rather than
100.0% identity. Without this option, a single mismatch in 10,000
residues displays 100% identity, with the option, 99.9% identity is
displayed (even though the identity is 99.99%).
[cal_consf.c]
Fix the false error message "code begins with 0" in cal_consf.c.
>>Feb. 12, 2014
[compacc2.c]
When providing "sequence length" to annotation scripts, add offsets.
Also modify scripts to allow sequence lengths to increase.
>>Jan. 28, 2014 (re-released as fasta-36.3.6d/Jan 2014)
[dropfs2.c, calconsf.c, tatstats.c]
The coordinate fix for fasts36/fastm36 (Dec 18, 2013) broke some
fasts/fastm alignments. The alignment code has been reverted to the
"classic" code that has been used for more than 10 years. However,
that code always marked the first aligned residue as 1, even when the
first part of the query did not align. The initial coordinate offset
has been fixed; the coordinate is now the position in the first
aligned fragment. This may be confusing, because with fasts, the
first aligned fragment may not be the first fragment in the query
list. The coordinate provided always provides the offset from the
beginning of the first fragment in the alignment, not the first
fragment in the list. This fix required changes to the definition of
calc_astruct(), which required changes to build_ares.c, mshowalign.c,
calc_cons.c, dropfx.c, and dropfz2.c.
>>Jan. 24, 2014
[mshowalign2.c]
Add checks to assumption that '>gi|12345' is an NCBI library entry.
[nmgetlib.c]
Fix for nmgetlib.c with -DMYSQL_DB
Some cleanup of old Makefiles.
>>Jan. 1, 2014
[url_subs.c]
Fix off by one in domain coordinates in display_domains().
>>Dec. 18, 2013
[dropfs2.c, cal_consf.c]
Fix problem with alignment display when query sequence is much longer than library sequence.
>>Dec. 11, 2013
[compacc2.c]
Modified save_best2() to correctly exclude sequences outside
-M n1_low-n1_high limits.
>>Nov. 8, 2013 (re-released as fasta-36.3.6d)
[ncbl2_mlib.c]
Fix problem with src_long8_read() where int/uint64_t seems to cause
problems with Linux intel icc. Using int/unsigned int solves the problem.
>>Nov. 1, 2013
[apam.c, ncbl2_mlib.c, map_db.c]
[apam.c ] Fix problem with query sequences and libraries that do not
end in newline ('\n'). [ncbl2_mlib.c, map_db.c] provide grouping for
shifts for byte extraction in src_int4/long8_read() to remove compiler
warnings. [map_db.c] Fix problem reading sequences for indexing that
caused crash.
>>Oct. 8, 2013 (released as fasta-36.3.6d)
[comp_lib9.c, initfa.c]
Modify initfa.c/re_ascii() function to avoid qascii[] characters that
had been remapped for annotations.
>>Oct. 4, 2013
[nmgetlib.c, ncbl2_mlib.c]
Modify nmgetlib.c/re_openlib() to re-use memory mapped file arrays.
This had been the intention for some time, but a check for libf != 0
prevented the memory mapped arrays from being reused. libf is no
longer checked, just mm_flag.
>>Sep. 26, 2013
[ncbl2_mlib.c]
Fix a bug in ncbl2_mlib.c/parse_fastadl_asn() that prevented
accessions longer than 20 characters in description lines from BLAST
formatted libraries.
[compacc2.c]
Fix a bug in compacc2.c/comment_var() that showed the wrong original
sequence in qVariant changes.
>>Sep. 2, 2013
[dropfs2.c]
Fix bug in dropfs2.c/init_work() that prevents correct tatusov
statistics with -z >10.
>>Aug. 21, 2013 (released as fasta-36.3.6c)
[comp_lib9.c]
Fix bug in comp_lib9.c/new_seqr_chain() that prevented memory from
being allocated to the chain if a memory mapped database was followed
by a non-memory mapped database.
>>Aug. 9, 2013
[scaleswn.c]
Ensure shift to MLE_STATS if too many scores are excluded by trimming.
>>July 31, 2013 (released as fasta-36.3.6b)
[url_subs.c]
Make JSON output for -m 6 (html) dependent on $ENV{JSON_HTML}. JSON
output is not currently used.
>>July 26, 2013
[mshowalign2.c, scripts/lavplt_svg.pl]
Correct offsets in -m 11 lav plots, and modify lav2plt.pl/
lavplt_svg.pl/ lavplt_ps.pl to reflect the corrections.
Move all perl scripts out of /src into /scripts.
>>July 19, 2013 (released as fasta-36.3.6a)
[compacc2.c, cal_cons.c, dropfx.c, dropfz2.c, build_ares.c]
Provide dynamic string allocation/dyn_strcat for annotation string
output. This fixes problems with long proteins with many domains or
other annotations, which were too long for the fixed annotation output
storage.
Version date updated to July, 2013.
Compiled and tested on Windows32.
>>July 8, 2013
[cal_cons.c, dropfx.c, dropfz2.c]
Properly terminate annotions with offsets [cal_cons.c], and with
domains beyond alignment [dropfx.c, dropfz2.c]
>>July 5, 2013 (released as fasta-36.3.6)
[comp_lib9.c, doinit.c, dropfx.c, dropfz2.c]
Fix conflict between -m 9 and -z -1; fix annotation display using
non-script annotations. Stop using calc_last_set in dropfx/fz2.c.
>>June 24, 2013
[scripts/ann_feats_up_www2.pl]
Add script (ann_feats_up_www2.pl) for annotating UniProt sequences using:
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprotkb".
>>June 6, 2013
[compacc2.c, cal_cons.c, initfa.c, dropfx.c, dropfz2.c]
Provide the -XNS/-XXS/-XN+/XX+ and -XND/-XXD/-XN-/-XX- options that
specify how N:N and X:X alignments are counted for similarity and
identity. By default, N:N (DNA) and X:X (protein) alignments are
considered identical, but not similar (because their scores are
typically negative to address statistical issues).
-XNS/-XXS/-XN+/-XX+ cause N:N/X:X alignments to be counted as similar,
even though their alignment are negative. Likewise,
-XND/-XXD/-XN-/-XX- cause N:N and X:X alignments to be considered
non-identical (and non-similar).
>>May 28, 2013
[url_subs.c]
do_url1() has been modified to: (1) require env($REF_URL, $SRCH_URL,
$SRCH_URL1) for these links to produce printout. (2) Link text is
surrounded by . (3)
do_url1() now produces output automatically, which can
be used to get all the information provided by earlier URL links.
>>May 29, 2013
[mshowalign2.c]
Re-instate code in showalign() to ensure that original bbp->rst is
used for first alignment, rather than that calculated by CHECK_SCORE
(which is used for later sub-HSP's). The CHECK_SCORE -S alignment
score is based on the non-S alignment, and is then re-scored with the
low-complexity -S matrix. But the best alignment excluding
low-complexity can have a higher score than the best all-complexity
alignment rescored with -S.
>>May 27, 2013
[mshowalign2.c, url_subs.c]
The plot_domain.cgi SVG code has been expanded to allow the domain
structure of the entire query and library sequence, not just the
aligned regions, to be displayed. Showing domains above the query or
below the library takes an additional 18 px in each direction (36
total); this size needs to be provided in the