Motif searches

[Kay Hofmann]

Jorgensen (Jorgensen at BIOSCIENCE.BIOLOGY.UTAH.EDU) wrote:

: Can anyone recommend an online motif searching program?  For example, is
: there a program out there that can identify EGF domains, SH2 domains, PEST
: sequences, EF hands, kinases, C2 domains, etc. given a protein sequence?

I would recommend to use the new PROSITE/Profile server at

  http://ulrec3.unil.ch/software/

Simple motifs like ATP-binding sites, Zn-fingers, EF-hands etc. can
be searched with one of the PROSITE/patterns servers like

  http://ulrec3.unil.ch/software/PSTSCAN_form.html     or
  http://expasy.hcuge.ch/sprot/scnpsit1.html

More divergent motifs like SH2, SH3, C2, kinases etc. can be searched
with the Profile part of PROSITE

  http://ulrec3.unil.ch/software/PFSCAN_form.html

PEST regions can be searched at 
 
  http://www.biu.icnet.uk/projects/pest/

and Coiled-Coil regions at

  http://ulrec3.unil.ch/software/COILS_form.html


A collection of these and related servers for protein analysis can be
found on my link page

  http://ulrec3.unil.ch/useful.html


I hope these suggestions are helpful.


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Kay Hofmann                                  Tel. +41 (21) 692-5892
Bioinformatics Group                         FAX  +41 (21) 652-6933
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