An algorithm for computing the restriction scaffold assignment problem in computational biology

Authors:
Justin Colannino;Godfried Toussaint
Affiliations:
School of Computer Science, McGill University, Montréal, Québec, Canada;School of Computer Science, McGill University, Montréal, Québec, Canada
Venue:
Information Processing Letters
Year:
2005

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Abstract

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 [J. Comput. Biol. 10 (2) (2003) 385] published an O(nlogn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n^2) time, improving the best previous complexity of O(n^3).