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© 1987 IRL Press Ltd.

Matching relational patterns in nucleic acid sequences

William Saurin and Philippe Marlière 1

Unité de Programmation Moléculaire et Toxicologie Génétique CNRS UA271, INSERM U163
1Unité de Biochimie Cellulaire CNRS UA1129, Institut Pasteur, 28 rue du Docteur Roux, Paris 75015, France

We describe a program that efficiently searches sequence data banks for complex patterns where sites are linked by common relations such as identity, complementarity or span. Its algorithm is closer to those of automatic demonstration than to the finite state machines used in fast pattern matching. The repertory of relations can be enriched at will without rewriting the core of the program. The program is written in Pascal-ISO and runs on a microcomputer.

Received on September 25, 1986; accepted on April 30, 1987

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