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Bioinformatics Advance Access published online on March 16, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl083
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Published by Oxford University Press 2006
Received February 10, 2005
Revised February 15, 2006
Accepted March 3, 2006

Article

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.
Mikhail A. Roytberg, E-mail: MRoytberg{at}impb.psn.ru


  Abstract

Motivation: Evaluating all possible internal loops is one of key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available (Lyngsø et al., 1999) 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 nucleotides, using a computer with 2Gb RAM. We also propose algorithms, each with the run-time O(M*log2L), which construct sets of conditionally optimal multybranch 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.

Availability: Executables of Afold software tool, precompiled for Linux and Windows, are available at ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold.

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

Associate Editor: Charlie Hodgman
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