Detecting long tandem duplications in genomic sequences.

BMC Bioinformatics
Eric AudemardThomas Faraut

Abstract

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. 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. 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 recoveri...Continue Reading

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Citations

Sep 7, 2014·Genome Biology and Evolution·Shao-Lun LiuKeith L Adams
Nov 8, 2012·Evidence-based Complementary and Alternative Medicine : ECAM·Jin-Yi HanMi Kyeong Lee
Nov 5, 2013·Depression Research and Treatment·Diana SarokhaniKourosh Sayehmiri
Dec 28, 2018·Journal of Experimental Botany·Dikran TsitsekianStamatis Rigas

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Methods Mentioned

BETA
Tandem Arrays
Tandem Array
Tandem Gene Array

Software Mentioned

DUST
BioPerl
Ensembl Plants
ReD Tandem
BLASTX
DAGchainer
mreps
PAML
Perl script
TBLASTX

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