title: SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.
abstract: BACKGROUND
  The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but also their potential secondary structures. Sankoff's algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required.
  
  
  RESULTS
  We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable with the much slower existing algorithms.
  
  
  BACKGROUND
  The web server of SCARNA with graphical structural alignment viewer is available at http://www.scarna.org/.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan. scarna@m.aist.go.jp
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Tabei
authors.forename: Koji
authors.initials: K
authors.lastname: Tsuda
authors.forename: Taishin
authors.initials: T
authors.lastname: Kin
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012313:RNA