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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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
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