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Designing ambiguous query sequence

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Sat Jul 17 06:51:16 EST 1993


In <1993Jul16.105641.18725 at rockyd.rockefeller.edu> myersm at hcx.rockefeller.edu writes:

> 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?

As to my knowledge FINDPATTERNS would be the best choice. We do similar
things here. Depending on the pattern you can get really huge result files.
Therefore we have some programs here to scan and extract relevant data
from FINDPATTERNS result files on a VAX/VMS platform. Perhaps you want
a copy?

Regards
 Christoph Gartmann


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