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Open Access Methodology article

A fast structural multiple alignment method for long RNA sequences

Yasuo Tabei12, Hisanori Kiryu2, Taishin Kin2 and Kiyoshi Asai12*

Author Affiliations

1 Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan

2 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan

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BMC Bioinformatics 2008, 9:33  doi:10.1186/1471-2105-9-33

Published: 23 January 2008



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 webcite.