The WormBase Converter is a tool for researchers who need to produce up-to-date lists of C. elegans genes, for example starting with a large list culled from the literature.
You can convert a "WormBase ID", a "Gene/Transcript/CDS Sequence Name" or a "Gene Name" into a
"WormBase ID", a "Gene Sequence Name" or a "Gene Name".
Moreover, if you don't known the type of ID used in a gene list, or if the list
is composed of genes with more than one type of ID, the tool can
automatically detect the different IDs.
WormBase Converter also allows the conversion
between the WormBase releases. You can convert a Gene ID from a specific
release (e.g. WS170) into another release (e.g. WS190 for a conversion,
or WS160 for a reverse-conversion). If you are not sure about the
release used in a gene list, the program can detect it.
If you use any of these tools, please cite the following article:
Engelmann et al. A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One (2011) 6(5):e19055
To install a stand-alone version, or your own client-server version of the programme, necessary if you plan to use EASE Manager (see below), please go to SourceForge and follow the instructions there. Note that since EASE only runs under Windows (sorry; we didn't write it!), please be sure to take one of the versions for Windows. To continue to be useful, WormBase Converter needs to be updated with every WormBase release. Because of occasional annotation anomalies and inconsistencies, with each update, files on the server need to be manually edited. This is explained in a specific addendum to the complete tutorial. As an alternative, if you do not need to be constantly up-to-date, we will endeavour to provide corrected update files on the SourceForge page every 5 WS releases. This would eliminate the need for manual correction.
We also offer the possibility of running
WormBase Converter via the CIML server, which should always be
up-to-date, or at least up-dated shortly after each WS release. To
use this
possibility, which for most users will be the simplest solution see the next section.
The CLIENT version should be installed on a your computer that will then connect to the CIML server, and so should always be up-to-date.
- First download the appropriate version (Windows, or Mac/unix/linux).
- Click on this link, or download these instructions to know how to configure the program.
- Then read the quick start guide.
To test for over-representation of functional categories of genes within a gene list, the Ewbank lab uses EASE, a stand-alone implementation of DAVID. As with any such class-testing tool, unless corrected, with changes in gene structure predictions and annotations, the results become more and more inaccurate. Beyond this, we wanted to create new functional classes, adding data from our own experiments and from the literature. We found that doing this was relatively cumbersome, so we devised EASE Manager, to facilitate the entry of new lists, and to ensure that our current annotations remained up-to-date as gene structures evolved. If you would like to install the EASE Manager, please see the next page.