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© 1988 IRL Press Ltd

Restriction map construction using a ‘complete sentences compatibility’ algorithm

Pierre Tuffery 1, Philippe Dessen 2, Claude Mugnier 3 and Serge Hazout 1,*

1Unité de Recherches Biomathématiques et Biostatistiques, INSERM U263, Université Paris 7, Tour 53, 2 place Jussieu, 75251 Paris Cedex 05, France
2Laboratoire de Biochimie, Ecole Polytechnique 91128 Palaiseau Cedex, France
3CITI2 45 rue des Saints-Pères, 75270 Paris Cedex 06, France

*To whom reprint requests should be sent.

We have developed a new algorithm ‘Complete sentences compatibility’ (CSC) which uses single and double digestion fragments to rapidly determine restriction maps of circular DNA. From possible combinations of fragments of each simple digestion, which we call ‘sentences of decomposition’, we construct a restriction map which combines the sentences while taking into account compatibility rules. The algorithm can also deal with experimental errors of fragment weight and can suggest solutions that account for non-readable bands (fragments of zero length or multiple bands) on the gel. Because experiments using pairs of restrictive enzymes often result in multiple solutions, a complementary algorithm tries to reduce the number of proposed solutions by establishing consensus maps. The restriction map construction algorithm was tested on real cases, some containing more than fifteen fragments. Execution times range from 1 – 10 s on an IBM PC compatible microcomputer.

Received on July 21, 1987; accepted on December 31, 1987

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