Consensus pattern searching

Tom Doak tom_doak at hlthsci.med.utah.edu
Mon Sep 12 10:53:18 EST 1994

In article <1994Sep12.100417.9727 at leeds.ac.uk> ,
bmb5meb at biovax.leeds.ac.uk writes:

>I am looking for a program that will run on a DEC Vax running VAX/VMS
>or a DEC Alpha running OpenVMS AXP v1.5 which will allow me to scan a
>database with consensus patterns. Preferably the program should allow 
>patterns with flexible gaps, etc., and needs to be able to handle a
>which contains ~85,000 sequences. Please post or e-mail any suggestions;
>help will be greatly appreciated.

I probably can't be of any direct help to you, we use the comercial GCG
package, which we like a lot, and which allows you to search with various
patterns, such as a consensus.  
But I wanted to point out that if you have a family of proteins aligned,
you are throwing out a lot of information by using the consensus, unless
the conservation is very high.  Better, IMO, is to use profile technology
(Gribskov, et al In Methods in Enzymology, 183;146-159 (1989)), which
takes into account far more of the allowed variation in a family
alignment than can be accounted for in the consensus of the alignment. 
GCG has an implementation of the Profile set of programs.

Tom Doak
SaltLakeCity, Utah
tom_doak at hlthsci.med.utah.edu

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