title: Detecting long tandem duplications in genomic sequences.
abstract: BACKGROUND
  Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication.
  
  
  RESULTS
  In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes.
  
  
  CONCLUSIONS
  ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.
authors.affiliation: Unité de Biométrie et Intelligence Artificielle, UR 875, INRA, Toulouse, France. Eric.Audemard@gmail.com
authors.forename: Eric
authors.initials: E
authors.lastname: Audemard
authors.forename: Thomas
authors.initials: T
authors.lastname: Schiex
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D012984:Software