Mapping DNA by stochastic relaxation: a new approach to fragment sizes.

Instead of the traditional manipulations with given fixed fragment lengths in the restriction map construction a method of varying the lengths is proposed and realized under the simulated annealing algorithm scheme. The described approach has no upper limit on the number of fragments mapped with even ordinary hardware. A program has been derived from the algorithm combined with the last-squares refinement procedure for both linear and circular maps. The algorithm's ability to pick up missed maps is illustrated and the problem of reducing the number of solutions is discussed.