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<p>Dear Ensembl developers and users,</p>
<p>I'm involved in some helminth genome sequencing projects in my group, and my colleague (Eleanor Stanley) has built an-house Compara database for these genomes, from which we have inferred orthologs.</p>
<p>I'm planning to to project protein names and GO terms across species. I know that the Ensembl team do this already, but can't find many details of how it's done on the web.</p>
<p>I'm wondering whether my plan is very different from the Ensembl one, here is what I'm thinking of doing:</p>
<p>(i) Projecting protein names: for each gene in a query species (eg. Strongyloides ratti), identify its one-to-one and many-S.ratti-to-one orthologs in C. elegans, S. mansoni, human, D. melanogaster, zebrafish in our local Compara database. Take a protein name from a curated UniProt entry for one of these orthologs (taking orthologs from those species in order of preference given above), and project it to the query gene. Give the projected protein name evidence code ECO:0000265 and give the UniProt accession of the source protein. If the same protein name is projected to several query genes, then number then with Arabic numerals, as described in the UniProt protein naming guide www.uniprot.org/docs/nameprot I couldn't find much information on the web about how Ensembl project protein names so am wondering is this very different?</p>
<p>(ii) Projecting GO terms: for each gene in a query species (eg. Strongyloides ratti), identify all its orthologs (one-to-one, one-to-many, many-to-one, many-to-many) in C. elegans, S. mansoni, human, D. melanogaster, zebrafish in our local Compara database. Take manually curated GO terms of types IDA/IEP/IGI/IMP/IPI (excluding 'protein binding') from the orthologs. For each pair of ortholog genes from two different species, find the last common ancestors of their GO terms in the GO hierarchy: project these ancestral GO terms to the query gene. Do this for each pair of ortholog genes from two different species. Give the projected GO terms evidence code 'IEA' and give the UniProt accessions of the source proteins. [Note: by transferring the last common ancestors of GO terms from orthologs from two different species, I hope to be conservative and just project GO terms that are likely to be conserved across species.] I found some information on how Ensembl project GO terms on the web (<a href="http://www.ebi.ac.uk/GOA/compara_go_annotations">http://www.ebi.ac.uk/GOA/</a><a href="http://www.ebi.ac.uk/GOA/compara_go_annotations">compara_go_annotations</a>), but am not sure if the GO hierarchy is used at all as in my idea, or if all GO terms are directly projected from orthologs to the query gene?</p>
<p>Is this very different to what the Ensembl team are doing? I would be very grateful to hear of any differences.</p>
<p>Kind Regards,</p>
<p>Avril</p>
<p>Avril Coghlan</p>
<p>Parasite Genomics Team</p>
<p>Sanger Institute </p>
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