Sorting by Transpositions is Difficult

TL;DR

This paper proves that the problem of sorting genomes by transpositions, a key task in comparative genomics, is NP-hard, resolving a 15-year open question about its computational complexity.

Contribution

It establishes the NP-hardness of the Sorting by Transpositions problem, a fundamental question in computational genomics.

Findings

Proves Sorting by Transpositions is NP-hard.

Shows related problem of sorting with a limited number of permutations is NP-hard.

Answers a long-standing open question in genome rearrangement complexity.

Abstract

In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is, according to numerous studies, a relevant evolutionary distance. The problem of computing this distance when genomes are represented by permutations, called the Sorting by Transpositions problem, has been introduced by Bafna and Pevzner in 1995. It has naturally been the focus of a number of studies, but the computational complexity of this problem has remained undetermined for 15 years. In this paper, we answer this long-standing open question by proving that the Sorting by Transpositions problem is NP-hard. As a corollary of our result, we also prove that the following problem is NP-hard: given a permutation pi, is it possible to sort pi using db(pi)/3 permutations, where db(pi) is the number of breakpoints of pi?