[Computational-biology] Re: Nucleotide Pairing

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Richard Horler wrote:
> 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

I am not sure if this will answer your questionn but you may try as
starting point:

http://openwetware.org/wiki/Wikiomics:RNA_homology_search

and RNAhybrid:
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Best,

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