A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications

Abstract : Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced strings, so that some elements may not be covered by any block. We present an efficient fixed-parameter algorithm for the parameters number k of blocks and maximum occurrence d of a letter in either string. We then evaluate this algorithm on bacteria genomes and synthetic data.
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https://hal.archives-ouvertes.fr/hal-00906903
Contributor : Guillaume Fertin <>
Submitted on : Wednesday, November 20, 2013 - 2:28:11 PM
Last modification on : Thursday, April 5, 2018 - 10:36:48 AM

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Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Irena Rusu. A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications. Springer. 13th Workshop on Algorithms in Bioinformatics (WABI2013), Sep 2013, Nice, France. 8126, pp.244-258, 2013, Lecture Notes in Bioinformatics. 〈10.1007/978-3-642-40453-5_19〉. 〈hal-00906903〉

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