motif search

[Gary Williams]

In article <t.j.keen-2403001759460001 at sjuh-pc151.leeds.ac.uk>,
Jeffrey Keen <t.j.keen at leeds.ac.uk> wrote:
>Can anyone suggest how I can search a nucleotide database with a short
>protein motif. I had a look at EMBOSS but didn't see anything that might
>do the job.

At least two EMBOSS programs might do the trick for you:
fuzzpro   search for a (PROSITE style) pattern in proteins
preg      search for a regular expression in proteins


Or perhaps you did mean motifs:
patmatdb  search a protein sequence database with a motif

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK