Asset Details
Do you wish to reserve the book?
Detecting long tandem duplications in genomic sequences
Hey, we have placed the reservation for you!
By the way, why not check out events that you can attend while you pick your title.
Oops! Something went wrong.
Looks like we were not able to place the reservation. Kindly try again later.
Are you sure you want to remove the book from the shelf?
Detecting long tandem duplications in genomic sequences
Do you wish to request the book?
Detecting long tandem duplications in genomic sequences
Please be aware that the book you have requested cannot be checked out. If you would like to checkout this book, you can reserve another copy
We have requested the book for you!
Your request is successful and it will be processed during the Library working hours. Please check the status of your request in My Requests.
Oops! Something went wrong.
Looks like we were not able to place your request. Kindly try again later.
Journal Article
Detecting long tandem duplications in genomic sequences
2012
Overview
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.
Publisher
BioMed Central,BioMed Central Ltd,BMC
Subject
