Consensus pattern searching

Mathew Woodwark woodwark at arcu.afrc.ac.uk
Tue Sep 13 08:43:07 EST 1994


Michael Beck, Leeds University , was looking for a program that would
allow him to search sequence databases with a consensus. There are two approaches
here that I can think of. 1) He generates a consensus sequence using GCGs LINEUP
or other Multiple alignment program, and then uses the consensus sequence to
 search the data libraries with BLAST or FASTA or he uses GCGs profilemake 
and then profilesearch to search the data libraries. I don't know if he has 
GCG on site, but if not, he can go to SEQNET (or even me if he is BBSRC funded!)
Be warned, though, there  is a big difference between the consesnsus gained
from character matching and that gained from using a symbol comparison table.
Cheers
Mathwe Woodwark




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