title: Pairwise sequence alignment using a PROSITE pattern-derived similarity score.
abstract: Existing methods for alignments are based on edition costs computed additionally position by position, according to a fixed substitution matrix: a substitution always has the same weight regardless of the position. Nevertheless the biologist favours a similarity according to his knowledge of the structure or the function of the sequences considered. In the particular case of proteins, we present a method consisting in integrating other information, such as patterns of the PROSITE databank, in the classical dynamic programming algorithm. The method consists in making an alignment by dynamic programming taking a decision not only letter by letter as in the Smith & Waterman algorithm but also by giving a reward when aligning patterns.
authors.affiliation: LaMI, Université d'Evry-Val d'Essonne, Cours Monseigneur Roméro, Evry, France. comet@lami.univ-evry.fr
authors.forename: J P
authors.initials: JP
authors.lastname: Comet
authors.forename: J
authors.initials: J
authors.lastname: Henry
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D012985:Software Design
chemical_list: D011506:Proteins