WormBase Converter


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

Download & Installation

To continue to be useful, WormBase Converter needs to be updated with every WormBase release. Since this software was first released, Wormbase has extensively altered the architecture of its ftp site, and the file structure. Because we have not been able to modify WormBase converter to accommodate all these changes, the stand-alone updating function no longer works. There are two solutions. The easiest is to use WormBase converter in Client mode and connect to the CIML server as described below. If for some reason you need to use a local server, download the WormBase releases package available on SourceForge. We will endeavour to provide update files on the SourceForge page every 5 WS releases. 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. Please note that the WormBase Converter documentation has not been revised to take these changes into account.

Running WormBase Converter via the CIML server, which should always be up-to-date, or at least up-dated shortly after each WS release is the simplest option for most users; see the next section.

WormBase converter CLIENT download & installation

CLIENT version

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. 

EASE and EASE Manager

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.