New & Noteworthy

Additional origin mapping data added to OriDB - Saturday, 6th October 2012

OriDB proposed origin sites have been updated to include sites predicted by two genome-wide studies:

- Szilard et al. Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX. Nature Structural & Molecular Biology (2010) vol. 17 (3) pp. 299-305

- Crabbé et al. Analysis of replication profiles reveals key role of RFC-Ctf18 in yeast replication stress response. Nat Struct Mol Biol (2010) vol. 17 (11) pp. 1391-7

This has resulted in additional origin sites and the reassignment of some 'dubious' sites as 'likely'.

In addition, data confirming the location of 59 origin sites from the following study has been included:

Müller and Nieduszynski. Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Research (2012) vol. 22 (10) pp. 1953-62.

This study also demonstrated that 58 'likely' origin sites do not have origin activity; these sites are all now listed as 'Dubious' in OriDB.

Conrad NieduszynskiOriDB Version : 2.1.0

A manuscript describing the updated and expanded OriDB has been published in Nucleic Acids Research - Saturday, 28th April 2012

Nucleic Acids Research have publish a manuscript describing the updated and expanded OriDB. This paper can be used as a reference for OriDB as a database.

Conrad NieduszynskiOriDB Version : 2.0.0

New OriDB design with additional features - Friday, 23rd September 2011

Version 2 of OriDB involved a complete rewrite of the code and database structures. These changes have allowed us to incorporate many new datasets, add additional functionality and expand to additional organisms.

Conrad NieduszynskiOriDB Version : 2.0.0

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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 up`date`s have been made to OriDB:
1. The list of origin sites has been up`date`d 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB 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 NieduszynskiOriDB Version : 1.0.0