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International Workshop on Algorithms in Bioinformatics

WABI 2008: Algorithms in Bioinformatics pp 87–98Cite as

Minimum Common String Partition Parameterized

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5251))

Abstract

Minimum Common String Partition (MCSP) and related problems are of interest in, e.g., comparative genomics, DNA fingerprint assembly, and ortholog assignment. Given two strings with equal symbol content, the problem is to partition one string into k blocks, k as small as possible, and to permute them so as to obtain the other string. MCSP is NP-hard, and only approximation algorithms are known. Here we show that MCSP is fixed-parameter tractable in suitable parameters, so that practical instances can be efficiently solved to optimality.

Supported by the Swedish Research Council (Vetenskapsrådet), grant no. 2007-6437, “Combinatorial inference algorithms – parameterization and clustering”.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Chalmers University, 41296, Göteborg, Sweden

    Peter Damaschke

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  1. Peter Damaschke
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Keith A. Crandall Jens Lagergren

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© 2008 Springer-Verlag Berlin Heidelberg

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Damaschke, P. (2008). Minimum Common String Partition Parameterized. In: Crandall, K.A., Lagergren, J. (eds) Algorithms in Bioinformatics. WABI 2008. Lecture Notes in Computer Science(), vol 5251. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87361-7_8

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  • DOI: https://doi.org/10.1007/978-3-540-87361-7_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87360-0

  • Online ISBN: 978-3-540-87361-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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