Restriction site mapping in CLP(R)

Abstract

The Restriction Site Mapping problem is an important computational problem in molecular biology. In this paper, we show how the problem can be viewed as a dynamic constraint satisfaction problem and present an elegant solution in CLP(R) which handles linear and circular mapping problems for two enzymes. Formulating map consistency with constraints leads to a uniform treatment of errors and allows all solutions consistent within the error bounds to be generated. The results show that the natural problem constraints are very effective in reducing the size of the search space.