title: Genome rearrangements with indels in intergenes restrict the scenario space.
abstract: BACKGROUND
  Given two genomes that have diverged by a series of rearrangements, we infer minimum Double Cut-and-Join (DCJ) scenarios to explain their organization differences, coupled with indel scenarios to explain their intergene size distribution, where DCJs themselves also alter the sizes of broken intergenes.
  
  
  RESULTS
  We give a polynomial-time algorithm that, given two genomes with arbitrary intergene size distributions, outputs a DCJ scenario which optimizes on the number of DCJs, and given this optimal number of DCJs, optimizes on the total sum of the sizes of the indels.
  
  
  CONCLUSIONS
  We show that there is a valuable information in the intergene sizes concerning the rearrangement scenario itself. On simulated data we show that statistical properties of the inferred scenarios are closer to the true ones than DCJ only scenarios, i.e. scenarios which do not handle intergene sizes.
authors.affiliation: Laboratoire d'Informatique Gaspard Monge, CNRS UMR 8049, Université Paris-Est, 5 Bd Descartes, Marne-la-Vallée, 77454, France. laurent.bulteau@u-pem.fr.
authors.forename: Laurent
authors.initials: L
authors.lastname: Bulteau
authors.affiliation: LINA UMR CNRS 6241, Université de Nantes, 2 rue de la Houssinière, Nantes, 44322, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Fertin
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive (LBBE), 43 boulevard du 11 novembre 1918, Villeurbanne, 69622, France.|Institut National de Recherche en Informatique et en Automatique (INRIA) Rhône-Alpes, 655 avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Tannier
mesh_terms: D000465:Algorithms; D015321:Gene Rearrangement / Q000235:genetics*; D016678:Genome; D054643:INDEL Mutation; D008957:Models, Genetic
keywords: DCJ; Genome rearrangements; Indels; Intergenic regions