A fast structural multiple alignment method for long RNA sequences

• Published in: BMC bioinformatics Vol. 9; no. 1; p. 33
• Main Authors: Tabei, Yasuo, Kiryu, Hisanori, Kin, Taishin, Asai, Kiyoshi
• Format: Journal Article
• Language: English
• Published: London BioMed Central 23.01.2008; BioMed Central Ltd; BMC
• Subjects: Algorithms; Base Sequence; Bioinformatics; Biomedical and Life Sciences; Chromosome Mapping - methods; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; DNA sequencing; Genetic algorithms; Genomics; Life Sciences; Methodology; Methodology Article; Microarrays; Molecular Sequence Data; Nucleotide sequencing; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment - methods; Sequence Analysis, RNA - methods; Japan; Progressive Alignment; Reference Alignment; Pairwise Alignment; Stem Fragment; Matthews Correlation Coefficient
• ISSN: 1471-2105; 1471-2105
• 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 .