title: ddbRNA: detection of conserved secondary structures in multiple alignments.
abstract: BACKGROUND
  Structured non-coding RNAs (ncRNAs) have a very important functional role in the cell. No distinctive general features common to all ncRNA have yet been discovered. This makes it difficult to design computational tools able to detect novel ncRNAs in the genomic sequence.
  
  
  RESULTS
  We devised an algorithm able to detect conserved secondary structures in both pairwise and multiple DNA sequence alignments with computational time proportional to the square of the sequence length. We implemented the algorithm for the case of pairwise and three-way alignments and tested it on ncRNAs obtained from public databases. On the test sets, the pairwise algorithm has a specificity greater than 97% with a sensitivity varying from 22.26% for Blast alignments to 56.35% for structural alignments. The three-way algorithm behaves similarly. Our algorithm is able to efficiently detect a conserved secondary structure in multiple alignments.
authors.affiliation: Telethon Institute of Genetics and Medicine, Via P Castellino 111, 80133 Naples, Italy. dibernardo@tigem.it
authors.forename: Diego
authors.initials: D
authors.lastname: di Bernardo
authors.forename: Thomas
authors.initials: T
authors.lastname: Down
authors.forename: Tim
authors.initials: T
authors.lastname: Hubbard
mesh_terms: D000465:Algorithms; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D024522:Genes, BRCA2; D008969:Molecular Sequence Data; D022661:RNA, Untranslated / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D022661:RNA, Untranslated