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.
Thanks for any help anyone can give.
University of Alabama at Birmingham
ElliotL at uab.edu