multiple seqs in fasta fmt...
gvasudevan at medarex.com
Wed Mar 19 18:16:40 UTC 2003
I would like to use pepinfo rather than pepwindow because, pepwindow uses Enakai.dat (Kyte-DooLittle) and I want to use Eaa_hydropathy.dat(consensus Eisenberg) used by pepinfo.
pepwindow -datafile Eaa_hydropathy.dat ( raises exception--
Uncaught exception: Assertion failed, raised at ajmem.c:93)
And I have 100s of seqs to calculate this.
From: Peter Rice [mailto:pmr at ebi.ac.uk]
Sent: Wed 3/19/2003 9:43 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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