A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications
Data Structures and Algorithms
2013-08-02 v1 Computational Engineering, Finance, and Science
Quantitative Methods
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.
Cite
@article{arxiv.1307.7842,
title = {A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications},
author = {Laurent Bulteau and Guillaume Fertin and Christian Komusiewicz and Irena Rusu},
journal= {arXiv preprint arXiv:1307.7842},
year = {2013}
}
Comments
Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013)