Skip to Main content Skip to Navigation
Journal articles

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

Guillaume Fertin 1 Géraldine Jean 1 Eric Tannier 2, 3 
3 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Background: 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 accuracyof inference methods (Biller et al. in Genome Biol Evol 8:1427–39, 2016; Biller et al. in Beckmann A, Bienvenu L, JonoskaN, editors. Proceedings of Pursuit of the Universal-12th conference on computability in Europe, CiE 2016, Lecturenotes in computer science, vol 9709, Paris, France, June 27–July 1, 2016. Berlin: Springer, p. 35–44, 2016). In this line, wedefine a new genome rearrangement model called wDCJ, a generalization of the well-known double cut and join (orDCJ) operation that modifies both the gene order and the intergene size distribution of a genome.Results: We first provide a generic formula for the wDCJ distance between two genomes, and show that computingthis 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.Conclusions: We provide theoretical and empirical bounds on the expected growth of the parameter at the centerof our FPT and ILP algorithms, assuming a probabilistic model of evolution under wDCJ, which shows that both thesealgorithms should run reasonably fast in practice.
Document type :
Journal articles
Complete list of metadata

Cited literature [12 references]  Display  Hide  Download
Contributor : Eric Tannier Connect in order to contact the contributor
Submitted on : Tuesday, June 6, 2017 - 12:13:22 PM
Last modification on : Friday, August 5, 2022 - 2:54:51 PM
Long-term archiving on: : Thursday, September 7, 2017 - 12:26:27 PM


Publisher files allowed on an open archive



Guillaume Fertin, Géraldine Jean, Eric Tannier. Algorithms for computing the double cut and join distance on both gene order and intergenic sizes. Algorithms for Molecular Biology, BioMed Central, 2017, 12, 16 (11 p.). ⟨10.1186/s13015-017-0107-y⟩. ⟨hal-01533200⟩



Record views


Files downloads