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, tfastx,
tfasty are similar to tblastn).
The current version of the FASTA package is fasta-36.3.8g, Oct. 2018
See doc/README_v36.3.8g.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
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