A fast structural multiple alignment method for long RNA sequences.

BMC Bioinformatics
Yasuo TabeiKiyoshi Asai

Abstract

Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses. We propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA). The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory. The proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.

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Citations

Nov 4, 2008·Molecular Biotechnology·Ajish D George, Scott A Tenenbaum
Sep 18, 2008·Bioinformatics·Robert K BradleyIan Holmes
Dec 20, 2008·Bioinformatics·Michiaki HamadaKiyoshi Asai
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Methods Mentioned

BETA
RNASampler

Software Mentioned

4SALE
RNAalifold
Murlet
ProbCons
MEA
ClustalW
MXSCARNA
RNASampler
FoldalgnM
CMfinder

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