Genome2OR

Genome2OR annotates olfactory receptor genes in chordate genomes to enable systematic identification and cataloging of functional genes and pseudogenes for comparative and evolutionary analyses.

Key Features:

• High-throughput annotation: Processed 1,695 chordate genomes from the NCBI Assembly database to identify olfactory receptor genes.
• Annotation yield: Identified 765,248 olfactory receptor genes, including 404,426 functional genes and 360,822 pseudogenes.
• Primary output — CORD: Produces the Chordata Olfactory Receptor Database (CORD) containing primary annotations and derivative data such as species images, cross-references to public databases, structural models of receptors, sequence similarity networks, and sequence profiles.
• Sequence similarity network analysis: Constructs a large-scale protein sequence similarity network of all annotated receptors and clusters it into 20 communities categorized by presence or absence in ray-finned and lobe-finned fish.
• Algorithms: Leverages nhmmer, MAFFT, and CD-HIT for systematic annotation and sequence processing.
• Functional inference: Sequence and structural model analyses support investigation of potential unique activation and desensitization mechanisms in olfactory receptors.

Scientific Applications:

• Comparative genomics: Enables cross-species comparison of olfactory receptor repertoires across chordates.
• Evolutionary analysis: Supports studies of gene family expansions, contractions, and pseudogenization within olfactory receptor families.
• Structure–function studies: Facilitates investigation of receptor activation and desensitization mechanisms using sequence data and structural models.
• Resource development: Provides a comprehensive database and derived datasets (networks, profiles, models) for downstream bioinformatic and evolutionary analyses.

Methodology:

Annotations were produced using nhmmer, MAFFT, and CD-HIT; a protein sequence similarity network was constructed for all annotated receptors and clustered into 20 communities; analyses used 1,695 chordate genomes from the NCBI Assembly database.