RNA Structure Comparison - (Jan/22/2003 )

I am doing research in RNA structure prediction and I am curious to know what methods other people use for comparison. I am familiar with standard sequence comparison methods (e.g. BLAST, CLUSTAL, T-COFFEE, etc), but there is a striking LACK of methods for making secondary structure comparisons between two RNA structures (whose structure has either been determined empirically or predicted). Sean Eddy's COVE is clever.. but not very accurate IMHO.

Any suggestions for this problem? What have you tried in the past that has either worked or failed?

As there are some bonds between RNA bases, such as A-U, G-C bonds, the traditional sequence comparision methods are not so reasonable. Some algorithms are available considering the bonds. Please google Kaizhong Zhang's website to get some information. I just finished a software to compute the optimal alignment between two RNA structures. We can discuss it later.

try the Zucker www site
it is superb for what you want
http://www.bioinfo.rpi.edu/~zukerm/rna/