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OriDB: a DNA replication origin database.

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.

Pubmed ID: 17065467

Authors

  • Nieduszynski CA
  • Hiraga S
  • Ak P
  • Benham CJ
  • Donaldson AD

Journal

Nucleic acids research

Publication Data

January 4, 2007

Associated Grants

None

Mesh Terms

  • Chromosomes, Fungal
  • Computer Graphics
  • DNA Replication
  • DNA, Fungal
  • Databases, Nucleic Acid
  • Internet
  • Replication Origin
  • Saccharomyces cerevisiae
  • User-Computer Interface