Agradecimentos: This study was supported by the National Council for Scientific and Technological Development - CNPq (Grant Nos. 400487/2016-0, 425340/2016-3, 140466/2018-5, and 304380/2018-0), the São Paulo Research Foundation - FAPESP (Grant Nos. 2015/11937-9, 2017/12646-3, and 2017/16246-0), the...

Agradecimentos: This study was supported by the National Council for Scientific and Technological Development - CNPq (Grant Nos. 400487/2016-0, 425340/2016-3, 140466/2018-5, and 304380/2018-0), the São Paulo Research Foundation - FAPESP (Grant Nos. 2015/11937-9, 2017/12646-3, and 2017/16246-0), the Brazilian Federal Agency for the Support and Evaluation of Graduate Education - CAPES, and the CAPES/COFECUB program (Grant No. 831/15)

During the evolutionary process, genomes are affected by various genome rearrangements, that is, events that modify large stretches of the genetic material. In the literature, a large number of models have been proposed to estimate the number of events that occurred during evolution; most of them...

During the evolutionary process, genomes are affected by various genome rearrangements, that is, events that modify large stretches of the genetic material. In the literature, a large number of models have been proposed to estimate the number of events that occurred during evolution; most of them represent a genome as an ordered sequence of genes, and, in particular, disregard the genetic material between consecutive genes. However, recent studies showed that taking into account the genetic material between consecutive genes can enhance evolutionary distance estimations. Reversal and transposition are genome rearrangements that have been widely studied in the literature. A reversal inverts a (contiguous) segment of the genome, while a transposition swaps the positions of two consecutive segments. Genomes also undergo nonconservative events (events that alter the amount of genetic material) such as insertions and deletions, in which genetic material from intergenic regions of the genome is inserted or deleted, respectively. In this article, we study a genome rearrangement model that considers both gene order and sizes of intergenic regions. We investigate the reversal distance, and also the reversal and transposition distance between two genomes in two scenarios: with and without nonconservative events. We show that these problems are NP-hard and we present constant ratio approximation algorithms for all of them. More precisely, we provide a 4-approximation algorithm for the reversal distance, both in the conservative and nonconservative versions. For the reversal and transposition distance, we provide a 4.5-approximation algorithm, both in the conservative and nonconservative versions. We also perform experimental tests to verify the behavior of our algorithms, as well as to compare the practical and theoretical results. We finally extend our study to scenarios in which events have different costs, and we present constant ratio approximation algorithms for each scenario

CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQ

400487/2016-0; 425340/2016-3; 140466/2018-5; 304380/2018-0

COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPES

831/15

FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP

2015/11937-9; 2017/12646-3; 2017/16246-0

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