multiple seqs in fasta fmt...
pmr at ebi.ac.uk
Thu Mar 20 11:44:43 UTC 2003
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:
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.
More information about the EMBOSS