Program to deal with SELEX results

Joe Kramer kramer at mcbsgi.bio.sunysb.edu
Wed May 25 03:29:06 EST 1994

>Detecting an RNA consensus sequence and structure in a family of SELEX
>babies is an open research problem. So far as I know, the best current
>solution is to do it by eye, guided by the output from an RNA folding

Turns out that I was directing this question to the net for someone else--A
DNA person who has used that gel shift/cut out band/gel shift/... procedure.
Personally I am interested in RNA,  but this person is not.  Are any of the
GCG suite programs well suited to aligning and deriving a consensus from a
set of small DNA sequences?  

>It might be useful
>to you, and it'd probably spur further development from me if people
>had a go at SELEX babies with my code.
>- Sean Eddy
>- MRC Laboratory of Molecular Biology, Cambridge, England

I will probably be in a position to try it out someday soon.  

Joe Kramer

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