program for Motif identification?

[Brian Foley]

Daniel S. Chen (dschen at corona.hsc.usc.edu) wrote:
: Hi.  I'm trying to analyze/characterize a protein and I am looking for 
: a way to
: search for motifs.  Specifically, I'm interested in a program that will

: Dan



The Protein Domain database PRODOM is now accessible on the Web at:

<a href=        http://www.sanger.ac.uk/~esr/prodom.html        >URL</a>


ProDom is a collection of protein domain families that have been generated
automatically from Swissprot by Blastp and the Domainer algorithm (See
Sonnhammer ELL & Kahn D (1994) Protein Science 3:482-492).

The ProDom WWW server allows you to query ProDom by keywords, Blast,
or directly with Swiss-prot acronyms.  It also makes it very easy to
retrieve and display the families.

The main new feature of ProDom (apart from being updated to Swiss-prot 28)
is that it now graphically displays the domain organization of Swiss-prot
sequences according to ProDom.  Also the algorithm has been improved to
cause less fragmentation of the sequences.

_______________
Erik Sonnhammer
Sanger Centre
Cambridge UK