title: Statistical confidence measures for genome maps: application to the validation of genome assemblies.
abstract: BACKGROUND
  Genome maps are imperative to address the genetic basis of the biology of an organism. While a growing number of genomes are being sequenced providing the ultimate genome maps-this being done at an even faster pace now using new generation sequencers-the process of constructing intermediate maps to build and validate a genome assembly remains an important component for producing complete genome sequences. However, current mapping approach lack statistical confidence measures necessary to identify precisely relevant inconsistencies between a genome map and an assembly.
  
  
  RESULTS
  We propose new methods to derive statistical measures of confidence on genome maps using a comparative model for radiation hybrid data. We describe algorithms allowing to (i) sample from a distribution of maps and (ii) exploit this distribution to construct robust maps. We provide an example of application of these methods on a dog dataset that demonstrates the interest of our approach.
  
  
  BACKGROUND
  Methods are implemented in two freely available softwares: Carthagene (http://www.inra.fr/mia/T/CarthaGene/) and a companion software (metamap, available at: http://snp.toulouse.inra.fr/~servin/index.cgi/Metamap).
authors.affiliation: INRA Toulouse-Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France. Bertrand.Servin@toulouse.inra.fr
authors.forename: Bertrand
authors.initials: B
authors.lastname: Servin
authors.forename: Simon
authors.initials: S
authors.lastname: de Givry
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D033481:Chromosomes, Mammalian; D003627:Data Interpretation, Statistical; D004285:Dogs; D005819:Genetic Markers; D016678:Genome; D021101:Radiation Hybrid Mapping / Q000379:methods; D012984:Software
chemical_list: D005819:Genetic Markers