[Bioperl-l] protein identification program for proteomics

[Val Curwen]

>>>> 
>>>> I am looking for a stand alone protein identification program for
>>>> proteomics written in Perl to run on my Linux box.  This program will
>>>> identify proteins based on their molecular weight, and their N-terminal,
>>>> or C-terminal sequence (a short one that you get from micro sequencing).
>>>> The program will search flat files of amino acids sequences from the
>>>> generic databases.

>>>
>>>I think Alan Bleasbly once wrote something like this, so there might be
>>>something in EMBOSS...

It isn't in perl, but this does sound rather like mowse (EMBOSS version 
is emowse), that uses peptide mass fingerprints following protease 
digestion to identify proteins - proteins can be identified by a 
very few experimentally determined fragment masses. Whether a 
single N/C terminal peptide with sequence information and whole 
sequence MW will be sufficient I don't know - I've forwarded the 
message on to Alan but he's in a meeting right now.

We have a mowse server at HGMP (you don't need to be registered to 
use it):

http://www.hgmp.mrc.ac.uk/Bioinformatics/Webapp/mowse/

At the moment that only searches a database of fragments derived from
OWL sequences. The version Alan has just checked into EMBOSS may well
be able to search others - but I'll have to check with him. EMBOSS is 
happy under Linux.

Hope this helps,

Val

Val Curwen
Bioinformatics, MRC HGMP-Resource Centre, 
Hinxton, Cambridge, CB10 1SB