Paper Info
Title
Incorporating intergenic regions into reversal and transposition distances with indels
Abstract
Problems in the genome rearrangement field are often formulated in terms of pairwise genome comparison: given two genomes G(1) and G(2), find the minimum number of genome rearrangements that may have occurred during the evolutionary process. This broad definition lacks at least two important considerations: the first being which features are extracted from genomes to create a useful mathematical model, and the second being which types of genome rearrangement events should be represented. Regarding the first consideration, seminal works in the genome rearrangement field solely used gene order to represent genomes as permutations of integer numbers, neglecting many important aspects like gene duplication, intergenic regions, and complex interactions between genes. Regarding the second consideration, some rearrangement events are widely studied such as reversals and transpositions. In this paper, we shed light on the first consideration and created a model that takes into account gene order and the number of nucleotides in intergenic regions. In addition, we consider events of reversals, transpositions, and indels (insertions and deletions) of genomic material. We present a 4-approximation algorithm for reversals and indels, a 4:5-approximation algorithm for transpositions and indels, and a 6-approximation for reversals, transpositions, and indels.
Year
DOI
Venue
2021
10.1142/S0219720021400114
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
Keywords
DocType
Volume
Genome rearrangements, reversals, transpositions, indels, intergenic regions
Journal
19
Issue
ISSN
Citations 
6
0219-7200
0
PageRank 
References 
Authors
0.34
0
4
Name
Order
Citations
PageRank
Alexsandro Oliveira Alexandrino103.38
Andre Rodrigues Oliveira206.76
Ulisses Dias34113.23
Zanoni Dias426244.40