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

TL;DR

This paper introduces a fixed-parameter algorithm for the NP-hard Minimum Common String Partition problem, extended to unbalanced strings, with applications to genome rearrangement analysis.

Contribution

It presents the first fixed-parameter algorithm for the problem considering unbalanced strings with parameters k and d, and evaluates its effectiveness on biological data.

Findings

Algorithm performs well on bacteria genomes

Effective for small values of k and d

Provides a new tool for genome rearrangement studies

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.