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• W2102695327 abstract "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(L3), L is the length of the RNA. Results: We propose a new algorithm for evaluating internal loops, its run-time is O(M*log2L), M&lt;L2 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*log2L). Availability: Executables of Afold software tool, precompiled for Linux and Windows, are available at . Contact: MRoytberg@impb.psn.ru Supplementary information:" @default.
• W2102695327 created "2016-06-24" @default.
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• W2102695327 date "2006-03-16" @default.
• W2102695327 modified "2023-10-03" @default.
• W2102695327 title "Analysis of internal loops within the RNA secondary structure in almost quadratic time" @default.
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• W2102695327 doi "https://doi.org/10.1093/bioinformatics/btl083" @default.
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