OriDB:A DNA replication origin database

Nieduszynski, Conrad A. ORCID: https://orcid.org/0000-0003-2001-076X, Hiraga, Shin Ichiro, Ak, Prashanth, Benham, Craig J. and Donaldson, Anne D. (2007) OriDB:A DNA replication origin database. Nucleic Acids Research, 35 (SUPPL. 1). D40-D46. ISSN 0305-1048

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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.

Item Type: Article
Additional Information: Funding Information: OriDB has been built on a large body of work only a fraction of which we have been able to mention here. We apologize to colleagues whose work has not been cited and remind readers that OriDB contains a more extensive and expanding list of cross-referenced citations. CAN is a Leverhulme Trust Early Career Fellow. ADD is Royal Society University Research Fellow. The contributions to this work by CJB and PAK were supported in part by Grant DBI-0416764 from the National Science Foundation. The Open Access publication charges for this article were waived by Oxford University Press.
Uncontrolled Keywords: genetics ,/dk/atira/pure/subjectarea/asjc/1300/1311
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 08 Sep 2022 08:31
Last Modified: 23 Sep 2022 02:47
URI: https://ueaeprints.uea.ac.uk/id/eprint/87894
DOI: 10.1093/nar/gkl758

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