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Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Overview of attention for article published in Algorithms for Molecular Biology, June 2017
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Title
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes
Published in
Algorithms for Molecular Biology, June 2017
DOI 10.1186/s13015-017-0107-y
Pubmed ID
Authors

Guillaume Fertin, Géraldine Jean, Eric Tannier, Guillaume Fertin, Géraldine Jean, Eric Tannier

Abstract

Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accuracy of inference methods (Biller et al. in Genome Biol Evol 8:1427-39, 2016; Biller et al. in Beckmann A, Bienvenu L, Jonoska N, editors. Proceedings of Pursuit of the Universal-12th conference on computability in Europe, CiE 2016, Lecture notes in computer science, vol 9709, Paris, France, June 27-July 1, 2016. Berlin: Springer, p. 35-44, 2016). In this line, we define a new genome rearrangement model called wDCJ, a generalization of the well-known double cut and join (or DCJ) operation that modifies both the gene order and the intergene size distribution of a genome. We first provide a generic formula for the wDCJ distance between two genomes, and show that computing this distance is strongly NP-complete. We then propose an approximation algorithm of ratio 4/3, and two exact ones: a fixed-parameter tractable (FPT) algorithm and an integer linear programming (ILP) formulation. We provide theoretical and empirical bounds on the expected growth of the parameter at the center of our FPT and ILP algorithms, assuming a probabilistic model of evolution under wDCJ, which shows that both these algorithms should run reasonably fast in practice.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 5 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 5 100%

Demographic breakdown

Readers by professional status Count As %
Student > Doctoral Student 2 40%
Student > Ph. D. Student 1 20%
Professor 1 20%
Unknown 1 20%
Readers by discipline Count As %
Computer Science 2 40%
Biochemistry, Genetics and Molecular Biology 1 20%
Unknown 2 40%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 June 2017.
All research outputs
#10,036,970
of 11,317,953 outputs
Outputs from Algorithms for Molecular Biology
#141
of 177 outputs
Outputs of similar age
#223,031
of 267,496 outputs
Outputs of similar age from Algorithms for Molecular Biology
#4
of 5 outputs
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