title: Rapid motif compliance scoring with match weight sets.
abstract: Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runtimes. The program MOTIF incorporates a weight matrix and a rapid, backtracking tree-search algorithm to score motif compliance with greatly enhanced performance while placing no constraints on the motif. In addition, any positions within a motif can be marked as 'inviolate', thereby requiring an exact match. MOTIF allows a choice of regular expression formats and can use both motif and sequence libraries as either targets or queries. Nucleic acid sequences can optionally be translated by MOTIF in any frame(s) and used against peptide motifs.
authors.affiliation: ZymoGenetics, Inc., Seattle, WA 98105.
authors.forename: D
authors.initials: D
authors.lastname: Venezia
authors.forename: P J
authors.initials: PJ
authors.lastname: O'Hara
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software