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Open Access Highly Accessed Methodology article

Detecting long tandem duplications in genomic sequences

Eric Audemard1*, Thomas Schiex1 and Thomas Faraut2*

Author Affiliations

1 Unité de Biométrie et Intelligence Artificielle, UR 875, INRA, Toulouse, France

2 Laboratoire de Génétique Cellulaire, INRA, Toulouse, France

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BMC Bioinformatics 2012, 13:83  doi:10.1186/1471-2105-13-83

Published: 8 May 2012

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.