title: RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments.
abstract: BACKGROUND
  During the past decade, new classes of non-coding RNAs (ncRNAs) and their unexpected functions were discovered. Stable secondary structure is the key feature of many non-coding RNAs. Taking into account huge amounts of genomic data, development of computational methods to survey genomes for structured RNAs remains an actual problem, especially when homologous sequences are not available for comparative analysis. Existing programs scan genomes with a fixed window by efficiently constructing a matrix of RNA minimum free energies. A wide range of lengths of structured RNAs necessitates the use of many different window lengths that substantially increases the output size and computational efforts.
  
  
  RESULTS
  In this article, we present an algorithm RNASurface to efficiently scan genomes by constructing a matrix of significance of RNA secondary structures and to identify all locally optimal structured RNA segments up to a predefined size. RNASurface significantly improves precision of identification of known ncRNA in Bacillus subtilis.
  
  
  METHODS
  RNASurface C source code is available from http://bioinf.fbb.msu.ru/RNASurface/downloads.html.
authors.affiliation: Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, 19 Bolshoy Karetny per., Moscow 127994 and Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobyevy Gory, Moscow 119991, Russia.
authors.forename: Ruslan A
authors.initials: RA
authors.lastname: Soldatov
authors.forename: Svetlana V
authors.initials: SV
authors.lastname: Vinogradova
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Mironov
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics*; D003198:Computer Simulation; D016680:Genome, Bacterial; D023281:Genomics; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022661:RNA, Untranslated