Fasta
Description
FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985.[1] Its legacy is the FASTA format which is now ubiquitous in bioinformatics.
Although there are a large number of programs in this package, they belong to three groups: (1) Traditional similarity searching programs: fasta36, fastx36, fasty36, tfastx36, tfasty36, ssearch36, ggsearch36, and glsearch36; (2) Programs for searching with short fragments: fasts36, fastf36, tfasts36, tfastf36, and fastm36; (3) A program for finding non-overlapping local alignments: lalign36. Programs that start with fast search protein databases, while tfast programs search translated DNA databases.
License
Free for non-commercial use
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of fasta and load default version of fasta as
module avail fasta/ # list available modules module load fasta # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail fasta
and choose explicit version you want to use.
Documentation
http://faculty.virginia.edu/wrpearson/fasta/