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 duplicat

SUBMITTER: Audemard E 

PROVIDER: S-EPMC3464658 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature