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© Oxford University Press

Rapid motif compliance scoring with match weight sets

Domenick Venezia and Patrick J. O'Hara

ZymoGenetics, Inc., 4225 Roosevelt Way NE, Seattle, WA 98105, USA

Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runfimes. 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.

Received on May 5, 1992; accepted on August 1, 1992

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