Nucleotide Pairing

[Richard Horler]

Hi

I was wondering if anyone knows of a software which would allow me to
compare sequences to look for the maximum RNA:RNA base pairing. i.e. if
I input two RNA sequences the program could run through all possible
alignments and determine which is most stable i.e. most cognate base
pairs preferably including the none standard Watson Crick base pairs.

Richard

[darked]

Post by Richard Horler
Hi
I was wondering if anyone knows of a software which would allow me to
compare sequences to look for the maximum RNA:RNA base pairing. i.e. if
I input two RNA sequences the program could run through all possible
alignments and determine which is most stable i.e. most cognate base
pairs preferably including the none standard Watson Crick base pairs.
Richard

Something has eaten me previous answer..

Well, you can try http://foldalign.ku.dk/

You will find more programs here:
http://openwetware.org/wiki/Wikiomics:RNA_secondary_structure_prediction

Best,

Darek Kedra
http://openwetware.org/wiki/Wikiomics