A fast structural multiple alignment method for long RNA sequences

作者：Tabei Yasuo; Kiryu Hisanori; Kin Taishin; Asai Kiyoshi^*

来源：BMC Bioinformatics, 2008, 9(1): 33.

DOI：10.1186/1471-2105-9-33

Background: 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. Results: 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. Conclusion: 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.

• 出版日期2008-1-23