Nucleic Acids Research, 2010, Vol. 38, Database issue D299 Figure 2. Sequence feature annotation for human proto-oncogene vav. Displayed is the feature annotation returned for UniProt identiﬁer VAV_HUMAN. Laying out each type and source of annotation against each other allows the user to easily cross-reference functional information. Clicking on domains brings up available functional descriptions and a link to the original resource. Detailed tables of assignments can be found in separate tabs. To aid users each family is given a unique colour that is consistent across the website; for CATH-Gene3D domains the colour-picking algorithm makes common superfamilies brighter, and ensures superfamilies within the same fold have similar hues. NEW DAS AND OTHER WEB SERVICES The current set of DAS sources provided by Gene3D and CATH can be viewed at: http://cathdb.info:9000. Recently added is the ‘gene3d_ensembl’ track, which can be queried with Ensembl protein identiﬁers to retrieve domain annotations and the results viewed in a DAS client. Gene3D also underpins the FuncNet pipeline for analysis of protein function (paper submitted). This resource integrates various orthogonal methods that predict functional associations between proteins. Gene3D provides the Gene Expression Comparison, homology inherited Protein–Protein Interactions and Co-occurrence of Domains Analysis services, which can be queried directly via SOAP services or together through the FuncNet front-end service. Please refer to the FuncNet website for more information (http://funcnet.eu/). RELEASE SCHEDULE AND VERSIONING As of Gene3D_v9.0.0 release numbering system has been stabilized to use a three-part identiﬁer—‘Gene3D_v#.#.#’. The ﬁrst part signiﬁes a major release, and is incremented if there is a potential change to the domain assignments for a given protein. This would be the case if there is a new CATH release or if there is a change to the domain- identiﬁcation protocol. The second number is incremented if new sequences are added to the database, such as a new set of Ensembl genomes; while the third is incremented if any imported annotation is updated or added. As such, there is no predeﬁned schedule for releases, but instead is done ‘as needed’. However, major releases are expected two to three times a year, while sequences will be updated more often. DISCUSSION The primary purpose behind the changes made to Gene3D is to help support the investigations of the biological and medical research communities. To this extent, Gene3D actively collaborates within several teams and networks, providing data and tools, including the FuncNet function prediction web services as well as a member of the InterPro consortium of protein family databases and the IMPACT network, and provides targets for structural determination through the NIH PSI2 project. We also provide individualized domain predictions and linked data sets on request. Possible examples are lists of domains that contain annotated active sites, or are adjacent to transmembrane regions. Through these collaborations we hope to extend the web platform to provide data in formats that can be used by the various research communities. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS We would like to thank the CATH team for their help; SIMAP for providing signiﬁcant computational services and annotations; Prof. David Jones for providing Disopred2 predictions; InterPro for reviews of the data quality; Alison Cuﬀ for advice on distant homologies