Alignment tool for short sequences??

Mark D. Garfinkel mg16 at
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 D. Garfinkel (e-mail: mg16 at Ask for PGP public key)
(c) 1997; all rights reserved. Permission granted for Usenet quotation.
Fed up with unsolicited commercial e-mail? Join CAUCE at

More information about the Methods mailing list