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OriDB: a DNA replication origin database.

Conrad A Nieduszynski1, Shin-ichiro Hiraga, Prashanth Ak

  • 1Institute of Medical Science, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK. conrad@oridb.org

Nucleic Acids Research
|October 27, 2006
PubMed
Summary
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OriDB is a new web resource cataloging DNA replication origins in Saccharomyces cerevisiae. It integrates data from multiple studies to provide comprehensive information on origin sites, aiding research into eukaryotic chromosome replication.

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Eukaryotic chromosome replication initiates at multiple sites known as replication origins.
  • The budding yeast Saccharomyces cerevisiae serves as a model organism for understanding replication origins, with numerous studies mapping their genome-wide locations.

Purpose of the Study:

  • To create a comprehensive, web-based catalog of confirmed and predicted DNA replication origin sites in Saccharomyces cerevisiae.
  • To integrate and standardize data from various studies to provide a unified resource for researchers.

Main Methods:

  • Collation of existing genome-wide datasets on replication origin locations from multiple studies.
  • Development of OriDB, a web-based database, to store and present origin site information.

Related Experiment Videos

  • Inclusion of data such as genomic location, replication timing, DNA sequence, DNA duplex destabilization (SIDD), and phylogenetic conservation.

    • Main Results:

    • OriDB provides a centralized repository of distinct DNA replication origin sites in Saccharomyces cerevisiae.
    • The database offers detailed information for each origin, including genomic context, sequence data, and functional properties.
    • OriDB facilitates community contributions and links to external resources like SGD and PubMed.

    Conclusions:

    • OriDB serves as a valuable resource for studying DNA replication origins in Saccharomyces cerevisiae.
    • The integrated data and user-friendly interface, including a Chromosome Viewer, enhance the study of genome-wide replication dynamics.
    • The platform supports ongoing research by providing accessible and comprehensive information on replication origins.