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Bioinformatics Advance Access originally published online on March 16, 2006
Bioinformatics 2006 22(11):1317-1324; doi:10.1093/bioinformatics/btl083
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Published by Oxford University Press 2006
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

Aleksey Y. Ogurtsov 1, Svetlana A. Shabalina 1, Alexey S. Kondrashov 1 and Mikhail A. Roytberg 2,*

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
2 Institute of Mathematical Problems in Biology, Russian Academy of Science Pushchino, Moscow Region, 142290, Russia

*To whom correspondence should be addressed.

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 ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold.

Contact: MRoytberg{at}impb.psn.ru

Supplementary information: ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold

Received on February 10, 2005; revised on February 15, 2006; accepted on March 3, 2006

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