[Bioperl-l] protein identification program for proteomics
Val Curwen <email@example.com>
Thu, 14 Sep 2000 11:44:18 +0100 (BST)
>>>> 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
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,
Bioinformatics, MRC HGMP-Resource Centre,
Hinxton, Cambridge, CB10 1SB