multiple seqs in fasta fmt...

Vasudevan, Geetha gvasudevan at
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.


-----Original Message-----
From:	Peter Rice [mailto:pmr at]
Sent:	Wed 3/19/2003 9:43 AM
To:	Vasudevan, Geetha
Cc:	emboss at
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?



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