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OriDB: a DNA replication origin database

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

Authors

Conrad A. Nieduszynski

Shin-ichiro Hiraga

Prashanth Ak

Craig J. Benham

Anne D. Donaldson



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.

Journal Article Type Article
Journal Nucleic Acids Research
Print ISSN 0305-1048
Electronic ISSN 0305-1048
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 35
Issue Databa
Article Number D40-D46
APA6 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), doi:10.1093/nar/gkl758
DOI https://doi.org/10.1093/nar/gkl758
Publisher URL http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D40
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf



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