Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/24323
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Finding approximate gene clusters with Gecko 3 (Forthcoming/Available Online)
Authors: Winter, Sascha
Jahn, Katharina
Wehner, Stefanie
Kuchenbecker, Leon
Marz, Manja
Stoye, Jens
Bocker, Sebastian
Contact Email: stefanie.wehner@stir.ac.uk
Issue Date: 26-Sep-2016
Publisher: Oxford University Press
Citation: Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J & Bocker S Finding approximate gene clusters with Gecko 3 (Forthcoming/Available Online), Nucleic Acids Research.
Abstract: Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.
Type: Journal Article
URI: http://hdl.handle.net/1893/24323
DOI Link: http://dx.doi.org/10.1093/nar/gkw843
Rights: © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Affiliation: Friedrich Schiller University of Jena
University of Bielefeld, Germany
Aquaculture
University of Bielefeld, Germany
Philipps University of Marburg
University of Bielefeld, Germany
Friedrich Schiller University of Jena

Files in This Item:
File Description SizeFormat 
nar.gkw843.full.pdf2.23 MBAdobe PDFView/Open


This item is protected by original copyright



Items in the Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

If you believe that any material held in STORRE infringes copyright, please contact library@stir.ac.uk providing details and we will remove the Work from public display in STORRE and investigate your claim.