Tag Archives: software

Where can I get orthologs?

There are several databases that include orthology prediction for fungi. These all have pros and cons. Some are more comprehensive and have many more species. Some are curated orthologies and paralogy which should be pretty stable. Some are automated and groupings and ortholog group IDs change at each iteration.

  • A phylogenetic approach from a Saccharomyces perspective is at PhylomeDB.
  • Fungal Orthogroups is based on Synergy algorithm from I. Wapinski formerly of the Regev group at the Broad Institutue.
  • Yeast gene order browser (YGOB) for Saccharomyces spp and CGOB for Candida spp.
  • OrthoMCL database based on whole genomes, not a ton of fungi but useful starting set.
  • Ensembl Genomes provides ortholog prediction as part of the Compara pipeline though there is a limited phylogenetic diversity in the current Ensembl Fungal genomes.
  • TreeFam has Saccharomyces cerevisiae and Schizosaccharomyces pombe as the two fungi included in the curated ortholog assignments and phylogenies.
  • SIMAP provides pre-computed similarities among all proteins in UniProt.
  • InParanoid provides a pretty comprehensive of available 100 whole genomes and many fungal genomes which I tried to help select.
  • JGI’s Mycocosm attempts to provide a fungal focused paralog/gene family look at clusters of genes based on whole genomes
  • E-Fungi is also an attempt at automated clustering with some fancy webservices logic.
  • Fungal Transcription Factor database focused just on families of transcription factors.

Some of these tools are better than others in terms of providing downloadable tables.  Another problem is what Identifiers are used. Many biologists are using gene names or Locus identifiers not UniProt/GenPept IDs to identify genes or proteins of interest.  So tools that just cluster UniProt data aren’t as useful as those which refer to the gene or locus names. Also, providing a way to download all the data from a comparison is important for further mining and grouping of the data or cross-referencing local datasets.  One-by-one plugging in geneids is not really a tool that respects the idea that your user wants to ask sophisticated queries.

Also – beware that some approaches are very much pairwise comparisons lists whereas others are finding orthologous groupings.  So if you want to fine the Rad59 ortholog from all fungi it may be easier or harder depending on the source.

[I may make this a static page in the future to allow for more detailed updating since I know the available resources wax and wane]