FlyBase has recently incorporated orthology data from the DRSC Integrative Ortholog Prediction Tool (DIOPT). This dataset integrates ortholog predictions between 8 species (D. melanogaster, H. sapiens and 6 other model organisms) from 10 individual tools (Compara, Homologene, Inparanoid, Isobase, OMA, OrthoDB, orthoMCL, Phylome, RoundUp and TreeFam). The DIOPT approach provides a comparison of orthology predictions originating from different algorithms based on sequence homology, phylogenetic trees or functional similarity. DIOPT data are now searchable directly in FlyBase through the new ‘Orthologs’ tab of our QuickSearch tool, and are shown explicitly within the ‘Orthologs’ section of D. melanogaster Gene Reports.
The new Orthologs QuickSearch tool is quick and intuitive to use: simply select an input species, enter one or more gene symbols/IDs, then select one or more output species. When the input species is D. melanogaster, there is a choice between searching the new DIOPT data or our existing OrthoDB-derived orthology calls. The OrthoDB-specific dataset comprises ~40 species, biased towards those that are closely related to D. melanogaster, and will be particularly relevant to researchers interested in orthology relationships between Drosophila species or related Diptera, for example.
The results page of a QuickSearch Orthologs search shows the list of ortholog predictions arranged by species, and includes links to report pages at the relevant species databases, NCBI, Ensembl and/or OMIM. For DIOPT-based searches, the number and list of individual ortholog prediction tools that support a given orthologous gene-pair relationship is given; links are also provided to an alignment between orthologous gene-pairs on the DIOPT site, and to FlyBase Gene Reports where a non-Drosophila gene has been expressed transgenically in flies. A similar presentation is used for DIOPT-based data within the ‘Orthologs’ section of D. melanogaster Gene Reports.
In addition to serving the core Drosophila community, our new orthology search tool will provide a convenient portal to FlyBase data for non-Drosophila researchers - they can search with a human/mouse/worm (etc) gene of interest and quickly access the available knowledge and reagents for the fly ortholog(s). The provision of extensive links within the results page to orthologous gene reports at external websites will further aid inter-species/database navigation.