multiple seqs in fasta fmt...

[Peter Rice]

Vasudevan, Geetha wrote:
> 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.

Ah ... but pepwindow can use any of the "Nakai et al." database of amino 
acid parameters - these used to be in a database called "NAKAI" but are 
now in one called "AAINDEX". EMBOSS has a program "aaindexextract" that 
takes data from this database and makes it available for pepwindow.

It appears this enhancement did not make it into the pepwindow 
documentation... it will do today!!!

1. FTP the AAINDEX database from Japan:

ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1

2. Run aaindexextract with the aaindex1 file as input (or ask whoever 
installs EMBOSS to run it)

3. Run pepwindow with -datafile swer830101 and (to match pepinfo) 
-hwindow 9 (or whatever value you use for -length in pepinfo)

This is the middle plot pepinfo produces.

... and of course we should look into why pepinfo and pepwindow use 
different window lengths, and different option names.

Hope this helps.

Peter Rice