title: A novel approach to local reliability of sequence alignments.
abstract: BACKGROUND
  The pairwise alignment of biological sequences obtained from an algorithm will in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation of the alignment, the local trustworthiness of the alignment has to be quantified.
  
  
  RESULTS
  We present a novel approach that attributes a reliability index to every pair of residues, including gapped regions, in the optimal alignment of two protein sequences. The method is based on a fuzzy recast of the dynamic programming algorithm for sequence alignment in terms of mean field annealing. An extensive evaluation with structural reference alignments not only shows that the probability for a pair of residues to be correctly aligned grows consistently with increasing reliability index, but moreover demonstrates that the value of the reliability index can directly be translated into an estimate of the probability for a correct alignment.
authors.affiliation: Complex Systems Division, Department of Theoretical Physics, University of Lund, Sölvegatan 14A, Sweden.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Schlosshauer
authors.forename: Mattias
authors.initials: M
authors.lastname: Ohlsson
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D003574:Cytochrome c Group / Q000235:genetics; D045362:Cytochromes c2; D030562:Databases, Protein; D017143:Fuzzy Logic; D008969:Molecular Sequence Data; D011336:Probability; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000706:statistics & numerical data*
chemical_list: D003574:Cytochrome c Group; D045362:Cytochromes c2