OmaDB

OmaDB provides an R interface to the Orthologous Matrix (OMA) database for programmatic retrieval of orthologs, hierarchical orthologous groups (HOGs), protein sequences and metadata, and evolutionary relationships across thousands of genomes.

Key Features:

• R interface to OMA REST API: Wraps the OMA REST API to enable scripted queries from R.
• Ortholog retrieval: Retrieves orthologous relationships between genes across species.
• Hierarchical Orthologous Groups (HOGs): Accesses HOGs to represent orthology at multiple taxonomic levels.
• Protein sequences and metadata: Downloads protein sequences and associated protein metadata from OMA.
• Evolutionary relationships: Retrieves evolutionary relationship data curated by OMA.
• Cross-species gene correspondences: Queries cross-species gene correspondences for comparative analyses.
• Support for phylogenetics and functional annotation: Provides data retrieval suited for phylogenetic reconstruction and functional annotation workflows.
• Genome-scale analyses: Enables access to OMA's curated orthology framework across thousands of genomes for genome-wide evolutionary studies.
• Bioconductor integration: Facilitates incorporation of OMA data into downstream Bioconductor-based analyses.

Scientific Applications:

• Comparative genomics: Retrieval of orthologs and HOGs for large-scale comparative genomic analyses across many genomes.
• Phylogenetics: Provision of orthologous sequences and evolutionary relationships for phylogenetic reconstruction.
• Functional annotation: Use of orthology and protein metadata to inform gene function prediction and annotation transfer.
• Genome-wide evolutionary analyses: Analysis of evolution at genome scale using curated orthology relationships from OMA.
• Cross-species gene correspondence mapping: Mapping genes between species to study conservation and divergence.

Methodology:

Implements an R client that wraps the OMA REST API to query and download orthologs, hierarchical orthologous groups (HOGs), protein sequences, protein metadata, and evolutionary relationship data.