BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts - Archive ouverte HAL Access content directly
Journal Articles PLoS ONE Year : 2016

BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts

(1, 2) , (2) , (3) , (3) , (1) , (2)
1
2
3

Abstract

Various types of genome and gene similarity networks along with their characteristics have been increasingly used for retracing different kinds of evolutionary and ecological relationships. Here, we present a new polynomial time algorithm and the corresponding software (BRIDES) to provide characterization of different types of paths existing in evolving (or augmented) similarity networks under the constraint that such paths contain at least one node that was not present in the original network. These different paths are denoted as Breakthroughs , Roadblocks, Impasses, Detours, Equal paths, and Shortcuts. The analysis of their distribution can allow discriminating among different evolutionary hypotheses concerning genomes or genes at hand. Our approach is based on an original application of the popular shortest path Dijkstra's and Yen's algorithms.
Fichier principal
Vignette du fichier
journal.pone.0161474.PDF (2.56 Mo) Télécharger le fichier
Origin : Publication funded by an institution
Loading...

Dates and versions

hal-01361753 , version 1 (07-09-2016)

Licence

Attribution - CC BY 4.0

Identifiers

Cite

Etienne Lord, Margaux Le Cam, Éric Bapteste, Raphaël Méheust, Vladimir Makarenkov, et al.. BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts. PLoS ONE, 2016, 11 (8), pp.e0161474. ⟨10.1371/journal.pone.0161474⟩. ⟨hal-01361753⟩
70 View
146 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More