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© IRL Press at Oxford University Press

An algorithm for searching restriction maps

Webb Miller , Jim Ostell 1 and Kenneth E. Rudd 2

Department of Computer Science, The Pennsylvania State University University Park, PA 16802
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20892
2Laboratory of Bacterial Toxins, Division of Bacterial Products, Center for Biologics Evaluation and Research, Food and Drug Administration Bethesda, MD 20892, USA

This paper presents an algorithm thai searches a DNA restriction enzyme map for regions that approximately match a shorter 'probe' map. Both the map and the probe consist of a sequence of address-enzyme pairs denoting restriction sites, and the algorithm penalizes a potential match for undetected or missing sites and for discrepancies in the distance between adjacent sites. The algorithm was designed specifically for comparing relatively short DNA sequences with a long restriction map, a problem that will become increasing common as large physical maps are generated. The algorithm has been used to extract information from a restriction map of the entire Escherichia coli genome.

Received on October 28, 1989; accepted on February 2, 1990

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