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© Oxford University Press

An algorithm for analysing probed partial digestion experiments

Richard M. Karp and Lee A. Newberg 1

Computer Science Division, University of California Berkeley, CA 94720, USA
1Biological Sciences Division, The University of Chicago Chicago, IL, 60636-5415, USA

A partial digestion of DNA (e.g. cosmid, Lambda, YAC, chromosome) is performed and the lengths of thoses fragments which hybridize to a labeled probe are measured using gel electrophoresis. We give an efficient algorithm that takes as input this experimental data and proposes one or more candidate solutions. Each solution designates the location of each restriction site and spec the endpoints of each fragment. (Further experiments can then be designed to select the correct solution from this small set of candidates.) The algorithm works well even when the experiment gives inexact values for the lengths.

Received on February 19, 1993; revised on April 28, 1994; accepted on April 30, 1994

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