Georg Fuellen wrote:
>> Hello,
>> We're looking for approaches to the alignment of RNA structures.
> The RNA structures may be represented by trees of
> structure features/nucleotides, or by expressions using brackets.
>> Up to now, we're aware of the following approaches:
> *Shapiro & Zhang (CABIOS, 6(4):309-318, 1990),
> *Hesper, Hogeweg & Konings (Mol. Biol. Evol. (1987) 4(3), 300-314),
> *Hogeweg & Stadler (implemented in RNAdistance in the Vienna package 1994).
I would seriously check out Sean Eddy's COVE package and RNABOB
Look down the page at
http://genome.wustl.edu/eddy/hmm.html
ewan
