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OriDB - The DNA Replication Origin Database


NAR Molecular Biology Database Collection entry number 931
Nieduszynski, Conrad; Siow, Cheuk; Nieduszynska, Sian; Müller, Carolin1
1Institute of Medical Science, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
2UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA

Database Description

OriDB provides a web-based catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast (S. cerevisiae). 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 accessible at http://www.oridb.org/.

Recent Developments

Upcoming extensions of OriDB will include the incorporation of additional budding yeast datasets and a parallel databases for fission yeast (S. pombe) replication origins (as datasets are described).

Acknowledgements

Funding for OriDB was provided by The Leverhulme Trust (CAN), The Royal Society (ADD) and a National Science Foundation Grant DBI-0416764 (CJB and PA).

References

1. Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD (2007) OriDB: a DNA Replication Origin Database. Nucleic Acids Res. 35: in press.


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