OrthoDB

OrthoDB catalogs orthologous genes—defined as genes inherited by extant species from a single gene in their last common ancestor—across a broad phylogenetic spectrum to support evolutionary biology and comparative genomics; as of release 9 (2016) it covers over 22 million genes from more than 5,000 species.

Key Features:

• Taxonomic coverage: Includes plants, archaea, viruses and eukaryotes such as arthropods, fungi, vertebrates and basal metazoans, encompassing over 22 million genes from more than 5,000 species (release 9, 2016).
• Ortholog grouping: Defines orthologs as genes inherited by extant species from a single gene in their last common ancestor and organizes genes into ortholog groups.
• Functional annotation integration: Integrates data from over 100 sources and assigns descriptive titles to approximately 87% of ortholog groups, including Gene Ontology and InterPro attributes.
• Evolutionary and homology data: Provides computed evolutionary annotations and supports sequence homology queries for studying gene evolutionary dynamics and relationships.

Scientific Applications:

• Comparative genomics: Enables comparison of orthologous genes across species to identify conserved and divergent gene functions.
• Evolutionary biology: Supports analyses of gene origin, conservation and evolutionary dynamics using ortholog groups and computed evolutionary annotations.
• Phylogenetic studies: Provides ortholog groupings and homology information useful for constructing and interpreting phylogenies.
• Functional genomics: Facilitates inference of gene function via orthology and integrated Gene Ontology and InterPro annotations.

Methodology:

Integrates data from over 100 external sources, computes evolutionary annotations, and provides sequence homology query capabilities.