Sorting genomes using almost-symmetric inversions

Authors:
Zanoni Dias;Ulisses Dias;Lenwood S. Heath;João C. Setubal
Affiliations:
University of Campinas;University of Campinas;Virginia Tech;Virginia Tech
Venue:
Proceedings of the 27th Annual ACM Symposium on Applied Computing
Year:
2012

Citing 6
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Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

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Abstract

Inversions are one of the most frequent large-scale rearrangements observed in actual genomes. While a large body of literature exists on mathematical problems related to the computation of the inversion distance between abstract genomes, these works generally do not take into account that most inversions in bacterial chromosomes are symmetric or roughly symmetric with respect to the origin of replication. We define a new problem: how to sort genomes (or permutations) using almost-symmetric inversions. We show an algorithm that can sort any permutation using only almost-symmetric inversions. Two variants of this algorithm are presented that have better performance in practice. We explore the question of determining the minimum number of almost-symmetric inversions needed to sort a genome by presenting lower and upper bounds and results for special permutation families. The results obtained are the first steps in exploring this interesting new problem.