The zero exemplar distance problem

TL;DR

This paper investigates the computational complexity of the Zero Exemplar Distance problem in genome comparison, proving NP-hardness in various cases, and provides polynomial-time algorithms for specific scenarios, advancing understanding in genome rearrangement models.

Contribution

The paper offers a simplified proof of NP-hardness for Zero Exemplar Distance, extends results to multichromosomal genomes without gene order, and introduces polynomial algorithms for certain cases.

Findings

Zero Exemplar Distance is NP-hard for monochromosomal genomes with up to two copies per gene.

NP-hardness extends to multichromosomal genomes without gene order.

Polynomial algorithms exist when each gene appears exactly once in one genome and at least once in the other.

Abstract

Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that \textsc{Zero Exemplar Distance} for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this paper, we give a very simple alternative proof of this result. We also study the problem \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order, and prove the analogous result that it is also NP-hard even if each gene appears at most two times in each genome. For the positive direction, we show that both variants of \textsc{Zero Exemplar Distance} admit polynomial-time algorithms if each gene appears exactly once in one genome and at least once in the other genome. In addition, we present a polynomial-time algorithm for the related problem \textsc{Exemplar Longest Common Subsequence} in the special case that each mandatory symbol appears exactly once in one input sequence and at least once in the other input sequence. This answers an open question of Bonizzoni et al. We also show that \textsc{Zero Exemplar Distance} for multichromosomal genomes without gene order is fixed-parameter tractable if the parameter is the maximum number of chromosomes in each genome.