An Algorithm for Computing the Restriction Scaffold Assignment Problem in Computational Biology

Let S and T be two finite sets of points on the real line with |S| + |T | = n and |S| > |T |. The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element s i of S to an element t j of T is |s i - t j |, i.e., the distance between s i and t j . In 2003 Ben-Dor, Karp, Schwikowski and Shamir [2] published an O(n logn) time algorithm for this problem. Here we provide a counter-example to their algorithm and present a new algorithm that runs in O(n ) time, improving the best previous complexity of O(n )