On Bubble Generators in Directed Graphs - Inria - Institut national de recherche en sciences et technologies du numérique Accéder directement au contenu
Communication Dans Un Congrès Année : 2017

On Bubble Generators in Directed Graphs

Résumé

Bubbles are pairs of internally vertex-disjoint (s, t)-paths with applications in the processing of DNA and RNA data. For example, enumerating alternative splicing events in a reference-free context can be done by enumerating all bubbles in a de Bruijn graph built from RNA-seq reads [16]. However, listing and analysing all bubbles in a given graph is usually unfeasible in practice, due to the exponential number of bubbles present in real data graphs. In this paper, we propose a notion of a bubble generator set, i.e. a polynomial-sized subset of bubbles from which all the others can be obtained through the application of a specific symmetric difference operator. This set provides a compact representation of the bubble space of a graph, which can be useful in practice since some pertinent information about all the bubbles can be more conveniently extracted from this compact set. Furthermore, we provide a polynomial-time algorithm to decompose any bubble of a graph into the bubbles of such a generator in a tree-like fashion.
Fichier principal
Vignette du fichier
On_Bubble_Generators_in_Directed_Graphs.pdf (314.28 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)
Loading...

Dates et versions

hal-01647516 , version 1 (24-11-2017)

Identifiants

Citer

Vicente Acuna, Roberto Grossi, Giuseppe F Italiano, Leandro Lima, Romeo Rizzi, et al.. On Bubble Generators in Directed Graphs. WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science, Jun 2017, Eindhoven, Netherlands. pp.18-31, ⟨10.1007/978-3-319-68705-6_2⟩. ⟨hal-01647516⟩
322 Consultations
203 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More