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

Justin Colannino, Godfried Toussaint

    Research output: Contribution to journalArticle

    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(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
    Volume95
    Issue number4
    DOIs
    StatePublished - Aug 31 2005

    Fingerprint

    Scaffold
    Computational Biology
    Scaffolds (biology)
    Assignment Problem
    Restriction
    Computing
    Costs
    Real Line
    Set of points
    Assign
    Counterexample
    Finite Set
    Assignment

    Keywords

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

    ASJC Scopus subject areas

    • Computational Theory and Mathematics

    Cite this

    An algorithm for computing the restriction scaffold assignment problem in computational biology. / Colannino, Justin; Toussaint, Godfried.

    In: Information Processing Letters, Vol. 95, No. 4, 31.08.2005, p. 466-471.

    Research output: Contribution to journalArticle

    Colannino, Justin ; Toussaint, Godfried. / An algorithm for computing the restriction scaffold assignment problem in computational biology. In: Information Processing Letters. 2005 ; Vol. 95, No. 4. pp. 466-471.
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