[Bio-software] Re: Identifying proteins form amino acid composition

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Wed Jun 13 10:27:55 EST 2007


On Jun 5, 2:21 pm, Astala Vista <r... from NOSPAMle.ac.uk> wrote:
> I have discovered a couple of independently published papers that
> describe the amino acid composition of a protein that is of interest to
> me. The approximate length of the protein is known in both cases and the
> pI has been determined in one case. I'd like to identify the protein
> from the composition data.
>
> I'm aware of the AACompIdent program available at Expasy
> (http://www.expasy.ch/tools/aacomp/), but I'm not convinced that it's
> doing exactly what I want. As far as I can tell, AACompIdent does not
> allow for the possibility that the protein whose composition you know
> might be derived from a larger protein by post-translational cleavage.
> What I'd like to do is a search similar to that carried out by
> AACompIdent, but using a sliding window whose size is set by the user.
>
> Any ideas?
>
> Thanks.

You may try to use pepstat from EMBOSS:
http://bioweb.pasteur.fr/docs/EMBOSS/pepstats.html

This will let you calculate compositions of any fragment you fancy
(some scripting required). The problem is that for any variable window
length you will get exponential number of fragments. So this is not
gone work for identification of a peptide from a large protein
database. You may think about filtering proteins by i.e cellular
localization  and cut only these where you may predict signal
peptide.

Hope it helps

Darek Kedra
--
wikiomics.org



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