title: Automatic extraction of reliable regions from multiple sequence alignments.
abstract: BACKGROUND
  High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked.
  
  
  RESULTS
  We have previously developed a method to automatically assess the accuracy and overall difficulty of multiple alignments. This was achieved by a per-residue comparison between alternate alignments of the same sequences. Here we present a key extension to this method, an algorithm to extract similarly aligned regions from several alignments and merge them into a new consensus alignment.
  
  
  CONCLUSIONS
  We demonstrate that the fraction of correctly aligned residues within the resulting alignments is increased by 25-100 percent compared to the original input alignments, as only the most reliably aligned parts are considered.
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. timolassmann@gmail.com
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Erik Ll
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D000465:Algorithms; D016384:Consensus Sequence; D016415:Sequence Alignment / Q000379:methods / Q000592:standards*; D012984:Software