Alignment tool for short sequences??

brett 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 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. 

Brett Lindenbach
Program in Immunology                              
Washington University - St Louis                  
brett at                             

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