Minimum common string partition parameterized
Paper i proceeding, 2008

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.

parameterized algorithm

genome rearrangement

comparative genomics


Peter Damaschke

Chalmers, Data- och informationsteknik, Datavetenskap

8th Workshop on Algorithms in Bioinformatics WABI 2008, Lecture Notes in Bioinformatics

Vol. 5251 87-98
978-3-540-87360-0 (ISBN)


Datavetenskap (datalogi)



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