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2007.06.07 -- This application has been archived. See a CSB staff member for help.

FASTA

We have installed the FASTA V3.1 program in the CSB. Both SGI and DEC versions are available, the setup file will call the correct executable.
The following executables are available: 

fasta3*
fasta3_t*
fastf3*
fastf3_t*
fastx3*
fastx3_t*
fasty3*
fasty3_t*
prss3*
ssearch3*
ssearch3_t*
tfasta3*
tfasta3_t*
tfastf3*
tfastf3_t*
tfastx3*
tfastx3_t*
tfasty3*
tfasty3_t*

Local documentation for FASTA is available on-line and man pages are available for fasta3, fastf3 and prss3.

To use FASTA in the CSB:

FASTA generally should be run in the batch queue system.

Local protein sequence libraries currently available are in /dbase/owl/

setup fasta (interactive)
or
source /srv/local/setup/fasta.set (in a command file).

A typical command would be

fasta3 -b 20 -O fasta.out -q bov_pep.seq /dbase/owl/owl_19980802 ktup 2

where the input file bov_pep.fasta is in FASTA syntax.

Note: If you publish results obtained from the use of BLAST please cite the following:

W. R. Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" Methods in Enzymology 183:63-98.

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Last Modified: Thursday, 07-Jun-2007 10:32:40 EDT by P. Fleming