title: A fast structural multiple alignment method for long RNA sequences.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan. tabei@cb.k.u-tokyo.ac.jp
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Tabei
authors.forename: Hisanori
authors.initials: H
authors.lastname: Kiryu
authors.forename: Taishin
authors.initials: T
authors.lastname: Kin
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*