ISSN: 1545-5963

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.144

Laurent Bulteau , Université de Nantes, Nantes

Minghui Jiang , Utah State University, Logan

ABSTRACT

Given two genomes possibly with duplicate genes, the exemplar distance problem is that of removing all but one copy of each gene in each genome, so as to minimize the distance between the two reduced genomes according to some measure. Let \textsc{$(s,t)$-Exemplar Distance} denote the exemplar distance problem on two genomes $G_1$ and $G_2$ where each gene occurs at most $s$ times in $G_1$ and at most $t$ times in $G_2$. We show that the simplest non-trivial variant of the exemplar distance problem, \textsc{$(1,2)$-Exemplar Distance}, is already hard to approximate for a wide variety of distance measures, including both popular genome rearrangement measures such as adjacency disruptions, signed reversals, and signed double-cut-and-joins, and classic string edit distance measures such as Levenshtein and Hamming distances.

INDEX TERMS

hardness of approximation, comparative genomics

CITATION

Laurent Bulteau, Minghui Jiang, "Inapproximability of (1,2)-Exemplar Distance",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol. , no. , pp. 0, 5555, doi:10.1109/TCBB.2012.144