Alignment tool for short sequences??

Mark D. Garfinkel mg16 at midway.uchicago.edu
Tue Sep 9 14:59:20 EST 1997


	We start with a high-complexity degenerate population of random-
sequence oligomers. Bind to our purified DNA-binding protein, affinity-
purify the bound DNA-protein complexes, use PCR to amplify the bound
population. Subject to another round of binding & purification. Repeat
several times, clone resulting oligomer population, verify that individual
clones gel-shift with our protein, sequence them. We expect that the
32-mers subjected to the selection will have perhaps 12-nt-long islands
of reasonably conserved sequence representing the consensus binding target.

	Anyone know of a suitable program that will stack up about 50
such 32-base sequences & slide them around, flipping Watson strands for
Crick strands as needed, to create the consensus??

	A URL for suitable shareware/freeware would be welcome.

Mark
-- 
Mark D. Garfinkel (e-mail: mg16 at midway.uchicago.edu. Ask for PGP public key)
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