From the software web site:

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. 


A full manual is available from


Lab Cluster

FASTA36 is accessed from the module command

module load fasta36

A typical invocation would be

fasta36 -s BP62 query.file library.file

The module load does not load any query or library files. 



FASTA36 is access from the module command

module load fasta36

This loads MPI versions of the FASTA36 tool set.

A typical invocation would be

 mpirun -np 4 fasta36_mpi -q seq/mgstm1.aa seq/prot_test.lseg

This command will be wrapped within a PBS script.

The module load does not load any query or library files. 


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