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Bioinformatics Advance Access originally published online on May 12, 2007
Bioinformatics 2007 23(14):1866-1867; doi:10.1093/bioinformatics/btm255
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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.


  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/

Contact: ctzhang{at}tju.edu.cn

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

Associate Editor: Alfonso Valencia

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

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