Abstract
BackgroundAligning 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.ResultsWe 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.ConclusionThe 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 .
Highlights
Aligning multiple RNA sequences is essential for analyzing non-coding RNAs
At the first stage of the progressive alignment, which corresponds to the bottom level of the guide tree, the pairs of RNA sequences are aligned by engineered Dynamic Programming (DP) algorithm of SCARNA's pairwise alignment
We have developed MXSCARNA, a new structural multiple aligner of RNA sequences, which progressively applies the pairwise alignment algorithm used in SCARNA
Summary
A fast structural multiple alignment method for long RNA sequences Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai*1,2. Address: 1Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan and 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan. Published: 23 January 2008 BMC Bioinformatics 2008, 9:33 doi:10.1186/1471-2105-9-33
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