a given environment, as shown in the Phenotypes section of the sidebar. Finally, the inset GBrowse frame shows the nature of the mutation for all alleles of the gene under consideration. In this example, we can navigate back and forth from phenotypes to stocks to alleles to sequences; thanks to the fact that the SM19 gene has been cloned by functional complementation (21). However many of the Paramecium genes that were identiﬁed by a genetic approach have not yet been cloned. The corresponding allele pages are not linked to sequences, and do not contain a GBrowse image. Finding genes by sequence homology The Blast navigation tab brings up a Blast server (currently, our implementation of NCBI’s wwwblast server) allowing the user to paste in a nucleotide or protein sequence and run a Blast search against the proteins predicted by the automated annotation of the genome sequence (14). The search results are linked to the corresponding ParameciumDB gene pages. Other features RNA interference data can be submitted to ParameciumDB using a form that can be found from the Tool page. The Tool page also provides access to bioinformatics services, e.g. a Smith Waterman alignment of two nucleotide sequences provided by the user. The alignment is presented along with a histogram of the lengths of stretches of identical nucleotides and shows their positions on the alignment. This tool is useful in designing RNAi reagents and interpreting RNAi experiments. PERSPECTIVES In the absence of a dedicated curator, many simple improve- ments to ParameciumDB are still low on our priority list, such as images for gene and allele pages to illustrate, respec- tively, the localization of gene products or the phenotypes of mutant cells. We made the decision not to attempt to curate the Paramecium literature, at least for the moment, though many cross-references are provided to other databases, and each allele page has a well-crafted query that successfully retrieves the relevant literature from PubMed. We prefer to concentrate our efforts on exploiting the full power of the Chado schema design by implementing the module that can handle MIAME-compliant transcriptome data and by inter- facing other tools with our Chado database, such as the SynView synteny viewer (24) and a complex query interface using BioMart (25). Our immediate plans for ParameciumDB development are outlined below. Re-annotation project The value of the Paramecium genome sequence for research and teaching is critically dependent on the quality of the gen- ome annotations. Although the currently available automated annotations are of very good quality, thanks to the combined use of many resources including a large cDNA collection (14), we are already aware of many gene models that will require human curation to resolve contradictory evidence. We have therefore begun adapting the Apollo Genome Editor Nucleic Acids Research, 2007, Vol. 35, Database issue D443 (26) to read and write directly to ParameciumDB. Our objective is to train interested members of the Paramecium research community so that they can use Apollo, from anywhere in the world, to edit gene models and save their edits back to an instance of ParameciumDB. We will use the open source BioPipe workﬂow management software (27) to build computational pipelines to ensure that our community curators are working with up-to-date annotation evidence. Improved phenotype descriptions The use of ontologies for phenotype description is a new and fast-moving ﬁeld. ParameciumDB’s use of ontologies requires further development for at least three reasons. First, we are not using the full power of the Relationship Ontology, which is critical for computations based on the phenotypes. Second, Paramecium Anatomy Ontology requires development in order to meet the Open Biomedical Ontologies (http://obo.sourceforge.net/) standards, e.g. most terms do not have deﬁnitions. Moreover, it may turn out to be preferable in the long run to integrate this ontology with the GO Cellular Component and Biological Process ontolo- gies. Finally, inclusion in ParameciumDB of the exponenti- ally growing corpus of RNAi data is forcing us to devise a way for database users to propose new phenotypes. The PheNote tool, currently under development (Mark Gibson, personal communication), may provide the means toward this end. ACKNOWLEDGEMENTS We wish to thank the GMOD project, FlyBase and other associated MODs for making ParameciumDB possible, and Lincoln Stein in particular for his support and encouragement. We gratefully acknowledge Brian O’Connor, Allen Day and Mark Gibson for designing software features and/or patches specifically for ParameciumDB. We are indebted to Genoscope in more ways than can be enumerated here, and in particular to Jean Weissenbach, Patrick Wincker and Vincent Scha¨chter for advice and support and Jean-Marc Aury, Olivier Jaillon and Benjamin Noe¨l for access to data before release of the genome sequence. We wish to thank all of our colleagues in the Paramecium GDRE consortium for making requests and providing criticism that have shaped the user interface. The Paramecium stock collection and genetic data were curated with the help of Janine Beisson and Franc¸oise Ruiz (CGM, Gif-sur-Yvette). We acknowledge financial support from the CNRS, the ACI IMPBio2004 Contract 14 to L.S. and the ANR Contract NT05-2_41522 to J.C. Funding to pay the Open Access publication charges for this article was provided by the ‘Action Concerte´e Incitative Informatique, Mathe´matique et Physique en Biologie Mole´culaire (IMPBio)’. Conflict of interest statement. None declared. REFERENCES 1. Be´termier,M. (2004) Large-scale genome remodelling by the developmentally programmed elimination of germ line sequences in the ciliate Paramecium. Res. Microbiol., 155, 399–408.