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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Sorting signed circular permutations by super short operations

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Author(s):
Oliveira, Andre R. [1] ; Fertin, Guillaume [2] ; Dias, Ulisses [3] ; Dias, Zanoni [1]
Total Authors: 4
Affiliation:
[1] Univ Estadual Campinas, Inst Comp, Campinas, SP - Brazil
[2] Univ Nantes, CNRS, UMR 6004, LS2N, Nantes - France
[3] Univ Estadual Campinas, Sch Technol, Limeira - Brazil
Total Affiliations: 3
Document type: Journal article
Source: Algorithms for Molecular Biology; v. 13, JUL 26 2018.
Web of Science Citations: 0
Abstract

Background: One way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. In this context, genomes can be represented as ordered sequences of genes, each gene being represented by a signed integer. If no gene is repeated, genomes are thus modeled as signed permutations of the form pi = (pi(1)pi(2) ... pi(n)), and in that case we can consider without loss of generality that one of them is the identity permutation iota(n) = (12 ... n), and that we just need to sort the other (i.e., transform it into iota(n)). The most studied genome rearrangement events are reversals, where a segment of the genome is reversed and reincorporated at the same location; and transpositions, where two consecutive segments are exchanged. Many variants, e.g., combining different types of (possibly constrained) rearrangements, have been proposed in the literature. One of them considers that the number of genes involved, in a reversal or a transposition, is never greater than two, which is known as the problem of sorting by super short operations (or SSOs). Results and conclusions: All problems considering SSOs in permutations have been shown to be in P, except for one, namely sorting signed circular permutations by super short reversals and super short transpositions. Here we fill this gap by introducing a new graph structure called cyclic permutation graph and providing a series of intermediate results, which allows us to design a polynomial algorithm for sorting signed circular permutations by super short reversals and super short transpositions. (AU)

FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC
FAPESP's process: 15/11937-9 - Investigation of hard problems from the algorithmic and structural stand points
Grantee:Flávio Keidi Miyazawa
Support type: Research Projects - Thematic Grants