Local FASTA search with multiple sequences

Cornelius Krasel krasel at wpxx02.toxi.uni-wuerzburg.de
Wed Mar 14 11:08:25 EST 2001

MarkMcClain <mark.mcclain at vanderbilt.edu> wrote:


> Is anyone aware of a way to input multiple sequences to FASTA running
> locally? I know that I can run multiple searches through a batch queue using
> the GCG programs, but I would much prefer to run the analysis on my desktop.

What about leaving all the sequence files separate and writing a small shell
script invoking fasta for each file? Or do I miss something?

Assuming you have a directory with a lot of sequences all called
[something].seq, the following should invoke fasta for each of them
and store the result in [something].seq.fasta, if I understand the
manpage correctly:

 #! /bin/sh
 for i in *.seq
     fasta [insert your favorite parameters here] -O $i.fasta $i


/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */
/* D-97078 Wuerzburg, Germany   email: krasel at wpxx02.toxi.uni-wuerzburg.de */
/* "Science is the game we play with God to find out what His rules are."  */


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