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Analysis of internal loops within the RNA secondary structure in almost quadratic time
Authors:Ogurtsov Aleksey Y  Shabalina Svetlana A  Kondrashov Alexey S  Roytberg Mikhail A
Institution:National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Abstract:MOTIVATION: Evaluating all possible internal loops is one of the key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available runs in time O(L(3)), L is the length of the RNA. RESULTS: We propose a new algorithm for evaluating internal loops, its run-time is O(M(*)log(2)L), M < L(2) is a number of possible nucleotide pairings. We created a software tool Afold which predicts the optimal secondary structure of RNA molecules of lengths up to 28 000 nt, using a computer with 2 Gb RAM. We also propose algorithms constructing sets of conditionally optimal multi-branch loop free (MLF) structures, e.g. the set that for every possible pairing (x, y) contains an optimal MLF structure in which nucleotides x and y form a pair. All the algorithms have run-time O(M(*)log(2)L).
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