Database Search for RNA Binding

Elliot Lefkowitz Elliot_Lefkowitz at micro.microbio.uab.edu
Wed Mar 12 12:26:17 EST 1997

Does anyone have a good way to search a nucleotide database for
sequences that would bind to a query RNA? This would require:

1.	Search using the complement of the query sequence when using
FastA or BLAST (no problem)
2.	Allow for G:U base pairing (Big problem)

I have tried to alter the symbol comparison tables to allow for G:U base
pairing (by allowing U-C and G-A matches), but this then also allows the
complement, C:A base pairing which I do not want.

Any ideas?

Thanks for any help anyone can give.


Elliot Lefkowitz
University of Alabama at Birmingham
ElliotL at uab.edu

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