Frequently Asked Questions

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Why does S. cerevisiae OriDB not contain the same replication origin sites (ARS) as SGD?

The Saccharomyces Genome Database (SGD) are in the process of adding the confirmed replication origin sites (ARS) shown in OriDB. The putative replication origin sites described in OriDB will only be added to SGD once they have been confirmed. As SGD includes the addition origin sites they will include links to the appropriate OriDB record.

How are replication origin sites named?

S. cerevisiae
Only confirmed replication origins have been named - this is Saccharomyces Genome Database (SGD) standard practice. Putative replication origins can conveniently be referred to either by a location based name (such as ARS at II-774 to refer to the origin 774 kb from the left end of chromosome II) or where available a proposed ARS name (proARS; e.g. proARS227).

S. pombe
The independent studies that identified S. pombe replication origins have used a range of naming conventions that have resulted in different names being assigned to the same origin. To consolidate replication origin naming in S. pombe we have assigned each S. pombe replication origin site a systematic name based upon the chromosome number (in roman numerals) and the chromosomal coordinate. Hence the origin on chromosome 1 at 3060 kb is named ori-I-3060.

What software do I need to view OriDB pages?

OriDB web pages can be viewed through any modern web browser. We have tested the pages on Safari v4+ (Mac OS X) and IE8+ (Windows) and have successfully viewed them with other browsers, such as Google Chrome v15 and Firefox v7 (Mac OS X and Windows). Most of the pages use Javascript and the graphics are in SVG format (for modern browsers) and VML format (for legacy browsers).

Why does my browser report a slow running script?

This message refers to the scripts that draw the graphic display of data. On slower computers or legacy web browsers these scripts may be reported as slow running. If you allow the script to continue running the graphics should load correctly.

How do I cite OriDB?

What reference should I use to refer to the OriDB database?
The 2007 Nucleic Acids Research Database Issue includes a paper describing OriDB. This paper can be used as a reference for OriDB as a database. See this page for studies that have cited OriDB.

How should I cite data found in OriDB?
OriDB is a collation of previously published data and at present does not include any unpublished results. Therefore you should cite the relevant original paper as shown on the Reference for this Origin tab page for each Origin Site.

Can OriDB display my published data?

Probably! Please contact us with additional data that you would like us to include in OriDB. We will give priority to genome-wide datasets, but will also include data relevant to individual origins where appropriate. If you have a large dataset that you would like to be available at the time of publication please contact us with as much advanced notice as possible.

Can OriDB display my unpublished data?

At present OriDB only includes published datasets. This ensures that all work has undergone peer review and saves us from having to make difficult calls as to which datasets warrant inclusion. However, we understand that there are high quality, unpublished datasets that would be of interest to OriDB users. Therefore, in the long term we may include a limited number of unpublished datasets where we feel there is good justification for doing so. Any such datasets will be clearly indicated.

What about other model organisms?

At present OriDB is limited to the budding yeast, S. cerevisiae, and the fission yeast, S. pombe. In the long term we would be interested in including other model systems as more data becomes available. If you have genome-wide DNA replication origin mapping data and/or are interested in collaborating on developing OriDB for other model systems please contact us.