title: Towards detection of orthologues in sequence databases.
abstract: BACKGROUND
  Numerous homologous sequences from diverse species can be retrieved from databases using programs such as BLAST. However, due to multigene families, evolutionary relationship often cannot be easily determined and proper functional assignment becomes difficult. Thus, discrimination between orthologues and paralogues within BLAST output lists of homologous sequences becomes more and more important.
  
  
  RESULTS
  We therefore developed a method that attempts to construct a reconciled tree from a gene tree of selected sequences and its corresponding phylogenetic tree of the species involved (species tree). An interface on the Web is developed to enable users to analyse the BLAST result. BLAST outputs are parsed and, for the selected sequences, multiple alignments are constructed either globally or for local regions. Bootstrapped trees are returned and compared with the expected species tree. In cases of discrepancies, gene duplications are assumed and a reconciled tree is computed. The reconciled tree shows probable orthologues and paralogues as predicted.
authors.affiliation: Biocomputing, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69012 Heidelberg, Germany.
authors.forename: Y P
authors.initials: YP
authors.lastname: Yuan
authors.forename: O
authors.initials: O
authors.lastname: Eulenstein
authors.forename: M
authors.initials: M
authors.lastname: Vingron
authors.forename: P
authors.initials: P
authors.lastname: Bork
mesh_terms: D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D019143:Evolution, Molecular; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012986:Software Validation