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Bioinformatics Advance Access published online on May 12, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm255
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© 2007 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.

DoriC: a database of oriC regions in bacterial genomes

Feng Gao and Chun-Ting Zhang *

Department of Physics, Tianjin University, Tianjin 300072, China

*To whom correspondence should be addressed. Dr. Chun-Ting Zhang, E-mail: ctzhang{at}tju.edu.cn


  Abstract

Summary: Replication origins (oriCs) of bacterial genomes currently available in GenBank have been predicted by using a systematic method comprising the Z-curve analysis for nucleotide distribution asymmetry, DnaA box distribution, genes adjacent to candidate oriCs and phylogenetic relationships. These oriCs are organized into a MySQL database, DoriC, which provides extensive information and graphical views of the oriC regions. In addition, users can Blast a query sequence or even a whole genome against DoriC to find a homologous one. DoriC will be updated timely and the latest version is DoriC 1.8, in which oriCs of 425 genomes (468 chromosomes) are identified.

Availability: DoriC can be accessed from http://tubic.tju.edu.cn/doric/.

Supplementary information: Supplementary information is available at http://tubic.tju.edu.cn/doric/supplementary.htm.

Associate Editor: Prof. Alfonso Valencia

Received on April 5, 2007; revised on April 29, 2007; accepted on May 4, 2007

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F. Gao and C.-T. Zhang
Origins of Replication in Sorangium cellulosum and Microcystis aeruginosa
DNA Res, May 12, 2008; (2008) dsn007v1.
[Abstract] [Full Text] [PDF]


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