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Nucleic Acids Research Advance Access published online on May 2, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn240
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes

Li-Wei Jiang1, Kuang-Lun Lin1 and Chin Lung Lu1,2,*

1Institute of Bioinformatics and 2Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5712121 ext. 56949; Fax: +886 3 5729288; Email: cllu{at}mail.nctu.edu.tw

Received February 2, 2008. Revised April 10, 2008. Accepted April 15, 2008.

OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. The overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, OGs are ubiquitous in microbial genomes and more conserved between species than non-OGs. Based on these properties, it has been suggested that OGs can serve as better phylogenetic characters than non-OGs for reconstructing the evolutionary relationships among microbial genomes. OGtree takes the accession numbers of prokaryotic genomes as its input. It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes. Next, OGtree computes an overlapping-gene distance between each pair of input genomes based on a combination of their OG content and orthologous OG order. Finally, it utilizes distance-based methods of building tree to reconstruct the genome trees of input prokaryotic genomes according to their pairwise OG distance. OGtree is available online at http://bioalgorithm.life.nctu.edu.tw/OGtree/.


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