profilesearch

[Richard Friedman]

Dear Pierre,

 The GCG profile program does not give a probability of the score
having occured randomly. You have to use the Z-scores of the sequences
from which you made your profile as a cutoff. If these sequences score
much higher than 3.0 (as I imagine they do) you can't regard your hit as

significant. Have you tried PSIBLAST, a profile method that gives
probability estimates? The web version is at:

http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-psi_blast

Documentation, including how to get the standalone version, which
runs faster than the web version is at

http://www.ncbi.nlm.nih.gov/BLAST/newblast.html

Best wishes,
Rich
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Richard Friedman
Herbert Irving Comprehensive Cancer Center Computer
and Informatics Resource Center
P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-1667 (voice) (212)305-6926 (fax)
friedman at cuccfa.ccc.columbia.edu


"I am sitting in the car with Isaac and Pinchas.
My flowery hat is on me. My jacket is on me."
 -Rose Friedman, age 21 months.