multiple seqs in fasta fmt...

[Wiepert, Mathieu]

Hi,

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.

-mat

-----Original Message-----
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)

But ...

it is (relatively) easy to modify pepwindow to generate hydropathy plots 
or data for multiple sequences.

How many sequences do you have in mind?

regards,

Peter