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Nucleic Acids Research Advance Access originally published online on October 25, 2006
Nucleic Acids Research 2007 35(Database issue):D40-D46; doi:10.1093/nar/gkl758
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Nucleic Acids Research, 2007, Vol. 35, Database issue D40-D46
© 2006 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.

Articles

OriDB: a DNA replication origin database

Conrad A. Nieduszynski*, Shin-ichiro Hiraga, Prashanth Ak1, Craig J. Benham1 and Anne D. Donaldson

Institute of Medical Science, University of Aberdeen Foresterhill, Aberdeen AB25 2ZD, Scotland, UK 1 UC Davis Genome Center, University of California at Davis One Shields Avenue, Davis, CA 95616, USA

*To whom correspondence should be addressed. Tel: +44 1224 555765; Fax: +44 1224 555844; Email: conrad{at}oridb.org

Received August 14, 2006. Revised September 5, 2006. Accepted September 27, 2006.

Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at www.oridb.org.


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