The FASTA (pronounced FAST-Aye, not FAST-Ah) programs are a comprehensive set of similarity searching and alignment programs for searching protein and DNA sequence databases. Like the BLAST programs blastp and blastn, the fasta program itself uses a rapid heuristic strategy for finding similar regions in protein and DNA sequences. But in addition to heuristic similarity searching, the FASTA package provides
programs for rigorous local (ssearch) and global (ggsearch) similarity searching, as well as a program for finding non-overlapping sequence similarities (lalign). Like BLAST, the FASTA package also includes programs for aligning translated DNA sequences against proteins (fastx, fasty are equivalent to blastx, and tfastx, tfasty are similar to tblastn).
See doc/README_v36.3.8i.md and doc/readme.v36 for a more complete summary of changes.
-
Changes to *_sse2 files to enable vectorized comparison on architectures other than Intel sse2 (e.g. ARM Neon). fasta-36.3.8i now incorporates the SIMDe (SIMD-everywhere, https://github.com/simd-everywhere/simde/blob/master/simde/x86/sse2.h) macro definitions that allow the smith_waterman_sse2.c, global_sse2.c, and glocal_sse2.c code to be compiled on non-Intel architectures (currently tested on ARM/NEON). Many thanks to Michael R. Crusoe (https://orcid.org/0000-0002-2961-9670) for the SIMDE code converstion, and to Evan Nemerson for creating SIMDe.
-
The code to read FASTA format sequence files now ignores lines with '#' at the beginning, for compatibility with PSI Extended FASTA Format (PEFF) files (http://www.psidev.info/peff).
- added options to -m8CB to (a) provide percent similarity as well as percent identity in blast tabular alignment output: '-m8CBs'; (b) add raw domain information '-m8CBd'; and (c) changed parsing after -m8CB so that any combination of 'l', 's', 'd', and 'L' (which is equivalent to 'ld') can be used in any order and combination.
-
fix a bug that appeared when multiple query sequences were searched against a large library that would not fit in memory. In that case, the number of library sequences and residues increased by the library size with each new search.
-
More consistent formats for *** ERROR and *** Warning messages.
-
Corrections to code to address compiler warnings with gcc8/9.
The major update in this release is the change of the license terms for the SSE2 accelerated versions of the Smith-Waterman and global/glocal alignment algorithms. All of the FASTA package is now distributed under open source licesnses, either Apache (for the majority of the code) or BSD (for the SSE2 accelerated code).
Bug fix to recover properly when memory mapped databases are too large.
Modifications to support makeblastdb format v5 databases. Currently, only simple database reads have been tested.
An updated release of the FASTA package (fasta-36.3.8h) is
available. In addition to minor bug fixes, the latest version can
generate query and library sequences using program scripts.
The latest version of the FASTA package is fasta-36.3.8h, Dec. 2018.
See doc/README_v36.3.8h.md for a more complete summary of changes.
The current released version of the FASTA package is fasta-36.3.8h, Nov. 2018
See doc/README_v36.3.8h.md for a more complete summary of changes.
The current version of the FASTA package is fasta-36.3.8g, Oct. 2018
See doc/README_v36.3.8h.md for a more complete summary of changes.
The current version of the FASTA package is fasta-36.3.8g, Apr. 2018
The current FASTA version is fasta-36.3.8g, Dec. 2017
The statistics routines for normally distributed scores (ggsearch36, glsearch36) are more robust to very low E()-value thresholds.
The current FASTA version is fasta-36.3.8f, Sept. 2017
If the -S option is used and a query sequence has no upper case letters, it is re-read with lower-case letters converted to upper-case.
The current FASTA version is fasta-36.3.8f, May. 2017
Various bugs in sub-alignment scoring corrected and support for the
EBI SP:GSTM1_HUMAN P09488 added. The format for the $SRCH_URL and
$SRCH_URL2 format strings has changed to enable pairwise alignment.
The fasta-36.3.6e version includes a new directory, psisearch2, with
scripts to run iterative PSSM (PSI-BLAST or SSEARCH36) searches using
an improved strategy for reducing PSSM contamination due to alignment
over-extension.
As of November, 2014, the FASTA program code is available under the Apache 2.0 open source license.
Up-to-date release notes are available in the file doc/readme.v36.
Documentation on the FASTA programs is available in the files:
| dir/file | description |
|---|---|
doc/fasta36.1 |
(unix man page) |
doc/changes_v36.html |
(short descriptions of enhancements to FASTA programs) |
doc/readme.v36 |
(text descriptions of bug fixes and version history) |
doc/fasta_guide.tex |
(Latex file which describes fasta36, and provides an introduction to the FASTA programs, their use and installation.) |
doc/fasta_guide.pdf1 |
(printable/viewable description of fasta-36) |
fasta_guide.pdf provides background information on installing the
fasta programs (in particular, the FASTLIBS file), that new users of
the fasta3 package may find useful.
Parts of the FASTA package are distributed across several sub-directories
| dir | description |
|---|---|
bin/ |
(pre-compiled binaries for some architectures) |
conf/ |
example FASTLIBS files (files for finding libraries) |
data/ |
scoring matrices |
doc/ |
documentation files |
make/ |
make files |
misc/ |
perl scripts to reformat -m 9 output, convert -R search.res files for 'R', and embed domains in shuffled sequences |
psisearch2/ |
perl/python scripts implementing the new psisearch2_msa iterative PSSM search |
scripts/ |
perl scripts for -V (annotate alignments) and -E (expand library) options |
seq/ |
test sequences |
src/ |
source code |
sql/ |
sql files and scripts for using the sql database access |
test/ |
test scripts |
For some binary distributions, only the doc/, data/, seq/, and bin/,
directories are provided.
To make the standard FASTA programs:
cd src
make -f ../make/Makefile.linux_sse2 all
where ../make/Makefile.linux_sse2 is the appropriate Makefile for your system.
The executable programs will then be found in ../bin
(e.g. ../bin/fasta36, etc.)
For a simple test of a program, try (from the src directory)
../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg