multiple seqs in fasta fmt...
Wiepert.Mathieu at mayo.edu
Wed Mar 19 17:47:50 UTC 2003
This may be simplistic, but I had the same problem with octanol, many fasta formatted sequence in one file. so I used seqretsplit on the file, and then did this at a command line
for i in *.fasta;do octanol -sequence $i -graph png –auto -goutfile2 $i.png;done
Not pretty, but it worked.
From: Peter Rice [mailto:pmr at ebi.ac.uk]
Sent: Wednesday, March 19, 2003 11:44 AM
To: Vasudevan, Geetha
Cc: emboss at hgmp.mrc.ac.uk
Subject: Re: multiple seqs in fasta fmt...
Vasudevan, Geetha wrote:
> Is it possible to read multiple seqs in fasta fmt to the emboss program "pepinfo"
> to produce a -goutfile for hydropathy values ?
No ... because pepinfo creates two graphs and making that work for
multiple sequence input is very tricky. This is why pepinfo only reads a
single sequence (but you can put ":id" after the filename to say which
FASTA file entry you want, of use dbifasta to index the file as a database)
it is (relatively) easy to modify pepwindow to generate hydropathy plots
or data for multiple sequences.
How many sequences do you have in mind?
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