Analysis of internal loops within the RNA secondary structure in almost quadratic time

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...

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Bibliographic Details
Published in:Bioinformatics Vol. 22; no. 11; pp. 1317 - 1324
Main Authors: Ogurtsov, Aleksey Y., Shabalina, Svetlana A., Kondrashov, Alexey S., Roytberg, Mikhail A.
Format: Journal Article
Language:English
Published: England Oxford University Press 01.06.2006
Oxford Publishing Limited (England)
Subjects:
Algorithms
Base Composition
Computational Biology - methods
Nucleic Acid Conformation
Programming Languages
RNA - chemistry
Software
Thermodynamics
ISSN:1367-4803, 1460-2059, 1367-4811
Online Access:Get full text
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Summary: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<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:
Bibliography:istex:48D30165AB8DD8ED5F24B984A3E5BC1A9E11BE61
To whom correspondence should be addressed.
Associate Editor: Charlie Hodgman
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btl083