Finding consensus seq in my protein

Sean Eddy eddy at wol.wustl.edu
Tue Dec 9 21:46:05 EST 1997


In article <Pine.A41.3.96.971208161754.333388A-100000 at tigger.cc.uic.edu> Michael Stockelman <michaels at uic.edu> writes:
  >	I have a protein sequence and also a published consensus sequence
  >(for the WD repeat)....
  >My question is, what computer program (preferably on a Mac or Win PC) can
  >find all the best repeats in my sequence?

If you're looking for common conserved protein domains in your
sequence, such as the WD repeat, consensus sequences are usually (but
not always) the best way to search; profile or HMM-profile methods are
typically more sensitive and specific.

You can access searchable profile databases on the Web in at least two
locations now:

The Pfam database is at:
	http://genome.wustl.edu/Pfam/
      or http://www.sanger.ac.uk/Pfam/

The ISREC Profiles database is at:
	http://ulrec3.unil.ch:80/profile/

disclaimer: I'm part of the Pfam consortium.

-- 

- Sean Eddy, Ph.D. 
- Dept. of Genetics, Washington University School of Medicine
- 660 S. Euclid Box 8232, St. Louis MO 63110, USA 
- mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy




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