Bioinformatic tools that are freely available to the research community.

1. ICeE: an interface for C. elegans experiments

ICeE is a database with a Web-browser interface that allows you to enter experiments for the nematode C. elegans and to search efficiently in this database. It's powered by PHP: Hypertext Preprocessor and uses a MYSQL database. The Web-browser interface is compatible with Firefox, Internet Explorer, Safari, Netscape, Google Chrome and Opera. It needs the activation of Javascript.

For more information, see the user manual.

ICeE is under the GNU General Public License.

Download the current version of ICeE

from

2. 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.

- convert different types of identifiers: a "WormBase ID" into "Gene Sequence Name", for example.

- convert lists of C. elegans genes from one WormBase release to another, taking into account changes in gene predictions.

3. EASE manager

A tool to facilitate the entry of new functional class lists into EASE, and to ensure that annotations remain up-to-date as gene structures evolve.

4. MosLocator

As part of the European project NEMAGENETAG, labs in Marseille, Lyon and Bristol worked together to produce a large collection of Mos1 insertion alleles. Most of these are publicly available. MosLocator is a tool for researchers who wish to look for insertions in or near one or many genes.

5. RNAi clone mapper

Making life easier when using RNAi clones. Originally designed for genome-wide screens. It does 3 things:

1. Automatically determines whether a clone taken from the Ahringer or Vidal RNAi library is what it is supposed to be, by mapping your clone sequences to our in-silico RNAi clone library.
2. Predicts gene targets for RNAi clones.
3. Allows multiple clone and transcript sequences to be retrieved.

6. 3PGA: 3^rd party genome annotation

Not yet ready!

References

Engelmann I, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ. (2011). A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One 6, e19055.

Frédéric Montañana, Renaud A Julien, Philippe Vaglio, Lisa R Matthews, Laurent Tichit, Jonathan J Ewbank (2014). ICeE: an interface for C. elegans experiments. Worm 3, e32160. http://dx.doi.org/10.4161/worm.32160

Thakur N, Pujol N, Tichit L, Ewbank JJ. (2014). Clone Mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans. G3 (Bethesda) pii: g3.114.013052.doi: 10.1534/g3.114.013052.

Vallin E, et al., (2012). A genome-wide collection of Mos1 transposon insertion mutants for the C. elegans research community. PLoS One 7, e30482.