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 ac...
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| Format: | Article |
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Oxford Journals
2007
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| Online Access: | https://eprints.nottingham.ac.uk/1203/ |
| _version_ | 1848790559127240704 |
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| author | Nieduszynski, Conrad A. Hiraga, Shin-ichiro Ak, Prashanth Benham, Craig J. Donaldson, Anne D. |
| author_facet | Nieduszynski, Conrad A. Hiraga, Shin-ichiro Ak, Prashanth Benham, Craig J. Donaldson, Anne D. |
| author_sort | Nieduszynski, Conrad A. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T18:14:32Z |
| format | Article |
| id | nottingham-1203 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T18:14:32Z |
| publishDate | 2007 |
| publisher | Oxford Journals |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-12032020-05-04T20:29:03Z https://eprints.nottingham.ac.uk/1203/ OriDB: a DNA replication origin database Nieduszynski, Conrad A. Hiraga, Shin-ichiro Ak, Prashanth Benham, Craig J. Donaldson, Anne D. 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. Oxford Journals 2007 Article PeerReviewed Nieduszynski, Conrad A., Hiraga, Shin-ichiro, Ak, Prashanth, Benham, Craig J. and Donaldson, Anne D. (2007) OriDB: a DNA replication origin database. Nucleic Acids Research, 35 (Databa). D40-D46. ISSN 0305-1048 http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D40 doi:10.1093/nar/gkl758 doi:10.1093/nar/gkl758 |
| spellingShingle | Nieduszynski, Conrad A. Hiraga, Shin-ichiro Ak, Prashanth Benham, Craig J. Donaldson, Anne D. OriDB: a DNA replication origin database |
| title | OriDB: a DNA replication origin database |
| title_full | OriDB: a DNA replication origin database |
| title_fullStr | OriDB: a DNA replication origin database |
| title_full_unstemmed | OriDB: a DNA replication origin database |
| title_short | OriDB: a DNA replication origin database |
| title_sort | oridb: a dna replication origin database |
| url | https://eprints.nottingham.ac.uk/1203/ https://eprints.nottingham.ac.uk/1203/ https://eprints.nottingham.ac.uk/1203/ |