Computing Similarity Between RNA Structures

News

Mar 6, 2000

We just got back from JCIS, where we presented this paper.

Dec 14, 1999

We are currently in the process of writing a new paper which incorporates some of our newer techniques for RNA computation. Most notably, we have introduced a constrained tertiary structure similarity measure, and we have shown that the optimal score between two RNAs is bounded below by our secondary structure computation, and bounded above by our new constrained tertiary structure computation. Obviously since the problem is NP-hard, we can only make an approximation of the optimal result, but we have found that in the vast majority of our test cases the upper and lower bounds are quite close, lending us a very nice "ballpark" figure.