title: Bayesian adaptive sequence alignment algorithms.
abstract: The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.
authors.affiliation: Wadsworth Center for Laboratories and Research, Albany, NY, USA.
authors.forename: J
authors.initials: J
authors.lastname: Zhu
authors.forename: J S
authors.initials: JS
authors.lastname: Liu
authors.forename: C E
authors.initials: CE
authors.lastname: Lawrence
mesh_terms: D000263:Adenylate Kinase / Q000235:genetics; D000465:Algorithms; D000595:Amino Acid Sequence; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D051528:Guanylate Kinases; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009703:Nucleoside-Phosphate Kinase / Q000235:genetics; D020653:Peptide Elongation Factor G; D010444:Peptide Elongation Factor Tu / Q000235:genetics; D010445:Peptide Elongation Factors / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D020653:Peptide Elongation Factor G; D010445:Peptide Elongation Factors; D000263:Adenylate Kinase; D009703:Nucleoside-Phosphate Kinase; D051528:Guanylate Kinases; D010444:Peptide Elongation Factor Tu