keggorthology

keggorthology assigns genes to KEGG Orthology (KO) groups using sequence similarity and functional annotation to enable cross-species functional mapping and integration into KEGG pathways.

Key Features:

• Orthology Classification: Assigns KEGG Ortholog IDs (KO identifiers) to gene families for cross-species comparison and functional annotation.
• Sequence Similarity and Functional Annotation: Groups genes into orthologous families based on sequence similarity searches and curated functional annotations.
• Pathway Integration: Maps KO groups onto KEGG metabolic and signaling pathway maps to analyze gene roles within biological networks.
• Interoperability with Bioconductor: Provides KO mappings usable within Bioconductor and R-based genomic analysis workflows.

Scientific Applications:

• Comparative Genomics: Identifies orthologous genes across species to support evolutionary and comparative genomics studies.
• Functional Annotation: Assigns functional information to genes through KO membership and conserved pathway context.
• Pathway Analysis: Enables analysis of metabolic and signaling processes by projecting gene sets onto KEGG pathways.

Methodology:

Performs sequence similarity searches and uses functional annotations to group genes into KO orthologous families and integrate them into the KEGG pathway database.