protein sequence generation

Peter Rice pmr at sanger.ac.uk
Fri Mar 26 11:41:18 EST 1999


Cornelius Krasel <krasel at wpxx02.toxi.uni-wuerzburg.de> writes:

> Peter Hufnagel <p_hufnagel at YAHOO.COM> wrote:
> > I am looking for a program to generate all possible
> > amino acid sequences that mach a given molecular weight
> > pluminus a certain tolerance.
> 
> Dependent on your given molecular weight, you might create an
> incredible amount of data. Be aware that for a protein with n
> residues there are approximately n! different sequences (somewhat
> less because of repetitions).

Protein mass spectrometry groups have been doing this for the past few
years. For example Matthias Mann's group at EMBL has a program
PeptideSearch and links to other similar applications.

	http://www.mann.embl-heidelberg.de/

All you need to do is reduce the original sequence (and any you
generate) to a composition instead (because the exact sequence does
not change the molecular weight.

Simply sorting the amino acids (A first, then C, the D) will be
enough.

Then all you need is the compositions that match the molecular weights.

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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