fasta36

Summary

Software Description

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 align- ments: lalign36. Programs that start with fast search protein databases, while tfast programs search translated DNA databases. Table I gives a brief description of the programs.

In addition, there are several programs included. map db is used to index FASTA format se- quence databases for more efficient scanning. lav2ps and lav2svg plot the .lav files produced by lalign -m 11 as postscript (lav2ps) or SVG (lav2svg) output.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load fasta36

Depending on where you are working, there may be more than one version of fasta36 available. To see which modules are available for loading you can run:

module avail fasta36