Sequence search with defined gap length

Rainer Blaesius rainer at med.unc.edu
Fri Jun 12 11:55:36 EST 1998


Hi,

does anyone of you know of a search algorithm available on the Internet
which is capable of searching for a peptide sequence in the public
databases with either defined numbers of Xs between conserved residues
or, ideally, even defined degenerate positions? To give an example, I am
looking for a way to find the following (arbitrary) sequences as similar
to a search sequence composed of :
Query AXCDXXGH:
Hit 1 AECDYYGH
Hit 2 AKCDAAGH
but not
       ACDGH or sequences with homologies to the Xs in my example.

Degenerate positions means that instead of Xs one could specify for a
given position (K or R), (I or V or L), etc.

If you know of this kind of Internet computing service I would
appreciate your comments!

Rainer




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