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

Justin Colannino, Godfried Toussaint

Research output: Contribution to journalArticle


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(nlogn) 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).

Original languageEnglish (US)
Pages (from-to)466-471
Number of pages6
JournalInformation Processing Letters
Issue number4
StatePublished - Aug 31 2005



  • Analysis of algorithms
  • Assignment problems
  • Computational biology
  • Computational geometry
  • Information retrieval
  • Operations research
  • Rhythmic similarity measures

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Signal Processing
  • Information Systems
  • Computer Science Applications

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