Designing ambiguous query sequence

Michael Myers myersm at hcx.rockefeller.edu
Fri Jul 16 09:56:41 EST 1993

A question for you experienced GCG users:

What is the best way to search the protein databases for matches to a
relatively short (about 20 amino acids) query sequence that contains
ambiguities and gaps? A hypothetical example might be the following:
Position 1 is some hydrophobic aa, positions 2-3 any aa, position 4 
always Lys, positions 5-6 any aa, postions 7-10 always Cys,Pro,Ala,Cys,
position 11 is Lys or Arg; etc.

I have read through the "Defining Patterns" section in the manual for the
program FindPatterns, which describes ambiguous expressions. Is this the 
method of choice, or are there other alternatives?

I'm sure this type of question has been posed before, but I have only
recently begun using/reading netnews. Direction to a specific FAQ would
be perfectly acceptable.

Thanks in advance,

Michael Myers
The Laboratory of Genetics 
The Rockefeller University
myersm at rockvax.rockefeller.edu

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