Typical uses
The OMA project provides different types of ortholog representations and tools, each useful for different contexts and applications. Here, we provide some examples of applications together with recommended solutions.
What would you like to do?
Appropriate orthology type
OMA groups that have a high-coverage of the species of interest.
Comments
Since, barring classification error, all sequence pairs within an OMA group are orthologs (and therefore related through speciation events), the corresponding gene tree is expected to follow the species tree.
Note that the full list of OMA groups can be downloaded in text or OrthoXML formats.
Appropriate orthology type
Ortholog view ("tab") for that particular gene (example for ADH1A_HUMAN).
Comments
This includes in-paralogs in the target genomes lineages with respect to the speciation event with the query genome.
Appropriate orthology type
Hierarchical group of human β-hemoglobin with "Tetrapoda" as taxonomic range.
Comments
This also retrieves γ-hemoglobin and ε-hemoglobin, which are thought to have diverged within the tetrapodes.
Appropriate orthology type
Comments
The viewer provides the genomic context of a particular entry and its orthologs in other species.
Appropriate orthology type
The free OMA standalone software package can infer pairwise orthologs, OMA groups, and hierarchical orthologous groups on custom data.
Comments
It is even possible to combine custom data with precomputed public data from OMA using the all-against-all export function.
Appropriate orthology type
Gene ontology annotations associated with a particular entry.
Comments
The view combines experimental and inferred annotations from UniProt-GOA as well as terms inferred from OMA orthologs.
Appropriate orthology type
Genome pair view, filtered to 1:1 orthologs.
Comments
According to current models, 1:1 orthologs are likely to have a similar function.
Appropriate orthology type
Comments
Orthologous genes can be used as anchor points.
Appropriate orthology type
Comments
Orthologs can be used to restrict the alignment search space. Thus, only conserved parts are used as anchors.