OriDB: a DNA replication origin database

Nieduszynski, Conrad A.; Hiraga, Shin-ichiro; Ak, Prashanth; Benham, Craig J.; Donaldson, Anne D.

Abstract

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.

Citation

Nieduszynski, C. A., Hiraga, S., Ak, P., Benham, C. J., & Donaldson, A. D. OriDB: a DNA replication origin database. Nucleic Acids Research, 35(Databa), Article D40-D46. https://doi.org/10.1093/nar/gkl758

• Journal Article Type: Article
• Deposit Date: Dec 16, 2009
• Journal: Nucleic Acids Research
• Print ISSN: 0305-1048
• Electronic ISSN: 0305-1048
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 35
• Issue: Databa
• Article Number: D40-D46
• DOI: https://doi.org/10.1093/nar/gkl758
• Public URL: https://nottingham-repository.worktribe.com/output/1017663
• Publisher URL: http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D40