Paper Info
Title
Sorting Permutations by Fragmentation-Weighted Operations
Abstract
One of the main problems in Computational Biology is to find the evolutionary distance among species. In most approaches, such distance only involves rearrangements, which are mutations that alter large pieces of the species' genome. When we represent genomes as permutations, the problem of transforming one genome into another is equivalent to the problem of Sorting Permutations by Rearrangement Operations. The traditional approach is to consider that any rearrangement has the same probability to happen, and so, the goal is to find a minimum sequence of operations which sorts the permutation. However, studies have shown that some rearrangements are more likely to happen than others, and so a weighted approach is more realistic. In a weighted approach, the goal is to find a sequence which sorts the permutations, such that the cost of that sequence is minimum This work introduces a new type of cost function, which is related to the amount of fragmentation caused by a rearrangement. We present some results about the lower and upper bounds for the fragmentation-weighted problems and the relation between the unweighted and the fragmentation-weighted approach. Our main results are 2-approximation algorithms for five versions of this problem involving reversals and transpositions. We also give bounds for the diameters concerning these problems and provide an improved approximation factor for simple permutations considering transpositions.
Year
DOI
Venue
2020
10.1142/S0219720020500067
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
Keywords
DocType
Volume
Approximation algorithms,genome rearrangements,permutations,reversals,transpositions,sorting distance,diameter
Journal
18
Issue
ISSN
Citations 
2
0219-7200
0
PageRank 
References 
Authors
0.34
0
3
Name
Order
Citations
PageRank
Alexsandro Oliveira Alexandrino103.38
Carla Negri Lintzmayer2269.14
Zanoni Dias326244.40