Alignment tool for short sequences??
brett at BORCIM.WUSTL.EDU
Tue Sep 9 15:29:17 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 midway.uchicago.edu. Ask for PGP public key)
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You could use GelAssemble & associated programs of the GCG suite, if you got
'em. I'd be pretty amazed if you find redundancy from such a massive library.
You'd need at least 100 micromoles of oligo to thoroughly cover that kind
of sequence space. Let us know if it works.
Program in Immunology
Washington University - St Louis
brett at borcim.wustl.edu
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