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New & Noteworthy

New OriDB available for budding yeast (S. cerevisiae) and fission yeast (S. pombe). - Monday, 20th February 2012
New OriDB pages are available for budding yeast (S. cerevisiae) and fission yeast (S. pombe). The old S. cerevisiae OriDB pages will remain here, but will no longer be actively maintained. Please update your links.
Conrad Nieduszynski
OriDB Version : 1.3.0
     
Tye lab study confirms 18 replication origin sites - Monday, 17th May 2010
Data from Bik Tye's group (Liachko et al., 2010) have been included in OriDB. These include the confirmation of 15 (previously 'likely') origin sites and the identification of 3 sites not previously identified as replication origins.
Thanks to Ivan Liachko and Bik Tye for communicating their data.
Conrad Nieduszynski
OriDB Version : 1.3.0
     
Fox lab study confirms 11 replication origin sites - Friday, 4th December 2009
Data from Catherine Fox's group (Shor et al., 2009) have been included in OriDB. These include the confirmation of 11 origin sites and the analysis of several origins by 2D gel. Shor et al. showed that a total of 14 sites do not have origin activity; these sites are all now listed as 'Dubious' in OriDB. Further data from this study will be available to download from OriDB soon.
Conrad Nieduszynski
OriDB Version : 1.2.0
     
OriDB genome annotation files now available for download - Tuesday, 15th July 2008
Files for genome annotation (currently only in BED format) are now available from here. From this page you can link directly to the UCSC genome browser annotated with a range of DNA replication data. Please let us know if there are additional files or formats that would be useful.
Conrad Nieduszynski
OriDB Version : 1.1.1
     
OriDB back - apologies for the break in service. - Saturday, 12th January 2008
We apologies for the short break in service experienced over the last 24 hours. Many thanks for all the people that alerted us to this problem.
Conrad Nieduszynski
OriDB Version : 1.1.1
     
'LinkOut' from PubMed directly to OriDB - Monday, 27th August 2007
OriDB curated papers (for example click here) can now be accessed directly from PubMed using the LinkOut facility. For an example of what the OriDB LinkOut looks like click here. To display OriDB LinkOuts by default in PubMed requires a 'My NCBI' account. More information is available from NCBI here.
Conrad Nieduszynski
OriDB Version : 1.1.1
     
OriDB curated paper links now available - Wednesday, 22nd November 2006
Details of OriDB curation of papers are now available. These pages can be accessed from each origin site record (using the reference tab) or from the yeast origin reference page by clicking on the study name. There is one page for each OriDB curated paper. These pages contain data from PubMed (including title, authors and abstract) and OriDB. These pages provide a new route in to Origin Sites. If you encounter any difficulties with these new pages or think that a study has been mis-annotated please contact OriDB.
Conrad Nieduszynski
OriDB Version : 1.1.1
     
New high-resolution origin mapping data available from Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio and Simon Tavare - Thursday, 26th October 2006
High-resolution mapping of ORC and Mcm2 binding sites and prediction of ARS consensus sequences (ACS) from the Aparicio and Tavare labs is published today in BMC genomics. More details are avilable here.
All the data from this study has been deposited with OriDB. The following updates have been made to OriDB:
1. The list of origin sites has been updated to include the new data.
2. Origin Summary Graphics tabs now display the new high-resolution ChIP data.
3. Origin Location Assignments tabs now include the data from this study (nimARS Study).
4. Origin Sequence Elements tabs now include the predicted ACS (nimACS) sites and additional confirmed ACS sites.
5. References for this Origin tab include Xu et al. (2006) where appropriate.
Please note: Addition of the full data from Xu et al. (2006) may take time. Currently the Chromosome Viewer does not display the new microarray data (this can only be viewed through each Origin Summary Graphics tab).
Conrad Nieduszynski
OriDB Version : 1.1.0
     
OriDB manuscript published in Nucleic Acids Research - Wednesday, 25th October 2006
Nucleic Acids Research today publish a manuscript describing OriDB. This paper can be used as a reference for OriDB as a database.
The Abstract is available here.
Full text is available here.
The PDF is available here.
Conrad Nieduszynski
OriDB Version : 1.0.0
     
OriDB manuscript accepted for publication in Nucleic Acids Research - Wednesday, 27th September 2006
Nucleic Acids Research have accepted for publication a manuscript describing the structure and functionality of OriDB. The paper, titled 'OriDB: a DNA Replication Origin Database', will appear in the 2007 database issue due out in January. A pre-publication version of the manuscript will be available here soon.
Conrad Nieduszynski
OriDB Version : 1.0.0
     
Addition of ARS600.2, ARS600.3 & ARS600.4 ARS assay details. - Tuesday, 19th September 2006
ARS600.2, ARS600.3 & ARS600.4 were assayed by Wyrick et al. (2001) and are now listed as confirmed origin sites. Note that the fragments cloned for ARS600.3 & ARS600.4 overlap by 195 bp and thus they could potentially represent the same origin. [Thanks to Jennifer Aparicio for this information.]
Conrad Nieduszynski
OriDB Version : 1.0.0
     
SGD pages now link to OriDB records - Friday, 15th September 2006
The Saccharomyces Genome Database (SGD) has expanded the list of ARS elements to include the majority of confirmed OriDB records. Each ARS element page provides a link to the appropriate OriDB page under the external links section. Please contact OriDB if one of these links fails to work correctly.
Conrad Nieduszynski
OriDB Version : 1.0.0
     

 

S. cerevisiae OriDB - v1.3.0.
Designed and maintained by Dr Conrad A. Nieduszynski & Dr Anne D. Donaldson