Counting sorting scenarios and intermediate genomes for the rank distance
File(s)TCBB3277733.pdf (914.48 KB)
Accepted version
Author(s)
Zanetti, Joao Paulo Pereira
Oliveira, Lucas Peres
Meidanis, Joao
Chindelevitch, Leonid
Type
Journal Article
Abstract
An important problem in genome comparison is the genome sorting problem, that is, the problem of finding a sequence of basic operations that transforms one genome into another whose length (possibly weighted) equals the distance between them. These sequences are called optimal sorting scenarios. However, there is usually a large number of such scenarios, and a naïve algorithm is very likely to be biased towards a specific type of scenario, impairing its usefulness in real-world applications. One way to go beyond the traditional sorting algorithms is to explore all possible solutions, looking at all the optimal sorting scenarios instead of just an arbitrary one. Another related approach is to analyze all the intermediate genomes, that is, all the genomes that can occur in an optimal sorting scenario. In this article, we show how to enumerate the optimal sorting scenarios and the intermediate genomes between any two given genomes, under the rank distance.
Date Issued
2023-05-01
Date Acceptance
2023-04-27
Citation
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 21 (3), pp.316-327
ISSN
1545-5963
Publisher
Association for Computing Machinery (ACM)
Start Page
316
End Page
327
Journal / Book Title
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume
21
Issue
3
Copyright Statement
Copyright © 2023 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/37200133
Subjects
Biochemical Research Methods
Bioinformatics
Biological cells
Breakpoint graph
Computer Science
enumeration
EVOLUTION
Extremities
genome rearrangements
Genomics
rank distance
REARRANGEMENTS
SCJ
Sorting
Space exploration
Statistics & Probability
Transforms
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2023-05-18