How do I find the ortholog / paralog / etc. of gene X?
We do not explicitly make ortholog assignments in WormBase. This is a non-trivial task and something that we leave to external experts whose results we try to make available. There are several sources that may be useful in WormBase. NCBI COGS, InParanoid and TreeFam are all programs that attempt to predict orthologous relationships. InParanoid and TreeFam are visible from the gene pages (see cdk-1 page for eg). The COGs are found on the respective protein page. inparanoid KOGs TreeFam There are also the precomputed BLAST results that are summarised on the gene pages. Each release we also produce a file of best blastp hits for each worm protein which can be found on the FTP site called best_blastp_hits.WSXXX.gz In addition we include since WS164 predicted orthologue assignemts based on Ensembl COMPARA which predicts orthology of the longest isoform based on homology as well as conserved gene order.
