is a Data Source.
It is part of the BER collection.
OMA (Orthologous MAtrix) is a database of orthologous genes among multiple species, providing a systematic classification of orthologs across complete genomes.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| oma.site | OMA Browser | home | Graphical Interface | http | Web interface for exploring OMA data |
| oma.api.rest | OMA REST API | api | Programming Interface | http | RESTful API for accessing OMA data |
| oma.api.sparql | OMA SPARQL | sparql | Programming Interface | http | SPARQL endpoint for accessing OMA data |
| oma.groups.txt | OMA Groups (Text) | oma-groups.txt.gz | Product | txt | OMA orthology groups in plain text fo... |
| oma.hogs.orthoxml | OMA HOGs (OrthoXML) | oma-hogs.orthoXML.gz | Product | xml | Hierarchical Orthologous Groups (HOGs... |
| oma.proteins.fasta | OMA Protein Sequences | oma-seqs.fa.gz (5.3 GB) | Product | fasta | Protein sequences from all genomes in... |
| oma.protein-annotations.txt | OMA Protein Annotations | oma-protein-annotations.txt.gz | Product | txt | Protein annotations in text format |
| oma.hdf5 | OMA Browser Database (HDF5) | current | Product | hdf5 | OMA Browser database in HDF5 format. ... |
| oma.rdf | OMA RDF Data | oma-rdf-turtle.tgz | Product | ttl | OMA data in RDF format (Turtle syntax) |
| oma.mapping.uniprot | OMA to UniProt Mapping | oma-uniprot.txt.gz | Mapping | tsv | Mapping of OMA identifiers to UniProt... |
| oma.mapping.ensembl | OMA to Ensembl Mapping | oma-ensembl.txt.gz | Mapping | tsv | Mapping of OMA identifiers to Ensembl... |
| oma.mapping.refseq | OMA to RefSeq Mapping | oma-refseq.txt.gz | Mapping | tsv | Mapping of OMA identifiers to RefSeq ... |
| oma.mapping.entrez | OMA to Entrez Gene Mapping | oma-entrez.txt.gz | Mapping | tsv | Mapping of OMA identifiers to Entrez ... |
| oma.mapping.go | OMA to GO Mapping | oma-go.txt.gz | Mapping | tsv | Mapping of OMA identifiers to Gene On... |
| oma.species.txt | OMA Species Metadata | oma-species.txt | Product | txt | Species metadata including taxonomy i... |
| oma.group-descriptions.txt | OMA Group Descriptions | group-descriptions.txt.gz | Product | txt | Text descriptions for OMA groups |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| rdf-portal.sparql.sib | RDF Portal SIB SPARQL Endpoint | sparql | Programming Interface | http | was derived from | SPARQL endpoint for SIB-derived RDF d... |
| hcop.web | HCOP Search | hcop | Graphical Interface | http | was derived from | HCOP web search for orthologs of one ... |
| hcop.all-seven-column | HCOP All Species Orthologs (7 column) | human_all_hcop_seven_column.txt.gz (25.2 MB) | Mapping | tsv | was derived from | All human ortholog assertions from HC... |
| hcop.all-sixteen-column | HCOP All Species Orthologs (16 column) | human_all_hcop_sixteen_column.txt.gz (39.9 MB) | Mapping | tsv | was derived from | All human ortholog assertions from HC... |
| hcop.species-downloads | HCOP Per-species Bulk Downloads | tsv | Product | http | was derived from | HCOP bulk downloads page with pre-com... |
OMA (Orthologous MAtrix) is a comprehensive database of orthologous gene relationships across multiple species. It provides a systematic and efficient approach to identifying orthologs among complete genomes, which are genes in different species that evolved from a common ancestor through speciation.
The OMA methodology employs an algorithm that starts with an all-against-all sequence alignment, followed by the identification of orthologous pairs and the construction of orthologous groups. The database includes:
OMA is maintained by the Dessimoz Lab at the University of Lausanne and the Swiss Institute of Bioinformatics (SIB), with biannual releases adding new genomes and improving data quality. The database is widely used for comparative genomics, phylogenetics, functional annotation transfer, and evolutionary studies.
Access to OMA data is provided through a user-friendly web interface, a REST API for programmatic access, and bulk downloads in various formats including text files, OrthoXML, FASTA, and RDF.
Created: May 07, 2025 | Last modified: September 23, 2026