- Genome Status
How can I find S. pombe orthologs for species other than human and S. cerevisiae?
For orthologs that are not manually curated by PomBase, we suggest two approaches:
You can search for orthologs/paralogs in Fungi, or in a pan-taxonomic comparison (eukaryotes), using Compara in the Ensembl browser.
- On any gene page, go to the Orthologs section (scroll or use the Quick Links box).
- Follow the relevant link to Compara - for fungal alignments, choose "View orthologs in other fungal species with Compara", or for all eukaryotic species choose "View orthologs across taxonomic space using pan-species Compara".
- You should see a "collapsed" gene tree highlighting your fission yeast gene of interest. From here you can click on any node to see a menu of options:
- Expand or collapes specific sub-nodes of the tree, or expand the tree fully
- View the alignment in FASTA format
- Launch the jalview multiple alignment viewer to see the full alignment and colour by residue conservation, hydrophobicity, etc.
To configure the protein entries visible in the alignment, select the most "inclusive" node you require. You can reduce the number of entries by collapsing individual sub-trees (step 4) before you generate your alignment. A brief video demostrates using the Compara trees.
Information about how the Compara trees are generated, homology types, and species is available from the Ensembl comparative genomics documentation.
From any gene page, follow the link to YOGY under External References.
YOGY is a web-based resource for retrieving orthologous proteins from ten eukaryotic organisms and one prokaryote: Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Dictyostelium discoideum, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Escherichia coli, Schizosaccharomyces pombe, and Saccharomyces cerevisiae. Using a gene or protein identifier from any of these organisms as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL