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 si of S to an element tj of T is |si - tj|, i.e., the distance between si and tj. In 2003 Ben-Dor, Karp, Schwikowski and Shamir [J. Comput. Biol. 10 (2) (2003) 385] published an O(n log n) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n2) time, improving the best previous complexity of O(n3).