Aligning Profiles

Elliot Lefkowitz lefkowitz at orion.cmc.uab.edu
Wed Jun 23 20:05:35 EST 1993


Does anyone know of a program which will align two profiles of
the
type generated by Michael Gribskov's Profile program? 

I have several groups of aligned sequences with a fair degree of
homology within each group. I am trying to determine if there is
any significant degree of homology between groups. I have
created
profiles of each group using ProfileMake (within the GCG
package)
and have compared the ProfileMake generated consensus sequence
of
one group with the profile of the other groups using ProfileGap.
The alignments obtained in one direction are somewhat different
than the alignment generated in the other direction. By directly
aligning profiles, I hope to be able to determine inter-group
homologies with a bit more certainty.

Thanks for any help anyone can give.

Elliot

**********************************************************
Elliot Lefkowitz, Ph.D.     |  University of Alabama      
Lefkowitz at Orion.cmc.uab.edu |  Department of Microbiology
205-934-1946                |  Birmingham, AL  35294
**********************************************************




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