BlastKOALA

BlastKOALA assigns KEGG Orthology (KO) identifiers to gene sequences to annotate and functionally characterize genomes and metagenomes.

Key Features:

• KO assignment: Assigns KEGG Orthology (KO) identifiers to input gene sequences for functional annotation.
• Modified KOALA algorithm: Uses a modified KOALA algorithm integrated with BLAST searches for sequence similarity-based KO assignment.
• Curated search database: Searches against a curated non-redundant dataset derived from the KEGG GENES database.
• Taxonomic organization: Maintains the dataset organized at species, genus, and family taxonomic levels and retains specific KO content for accurate annotation.
• Pathway and hierarchy mapping: Maps annotated genes onto KEGG pathways, BRITE hierarchies, and KEGG modules to reconstruct high-level biological functions.
• Compatibility with KEGG Mapper: Produces results usable with KEGG Mapper for comparative pathway analysis across organisms or samples.
• Related metagenome mode (GhostKOALA): GhostKOALA uses GHOSTX for faster database searches and extends the pangenome dataset with Cd-hit clusters including viral genes for metagenome annotation.

Scientific Applications:

• Genome annotation: Functional annotation of single-organism genomes by KO assignment.
• Metagenome annotation: Functional characterization of metagenomic datasets, including incorporation of viral genes via pangenome clusters.
• Pathway reconstruction: Reconstruction of metabolic and signaling pathways through mapping to KEGG pathways, BRITE hierarchies, and KEGG modules.
• Comparative pathway analysis: Comparison of pathway presence and composition across organisms or environmental samples using outputs compatible with KEGG Mapper.
• Evolutionary and functional genomics studies: Support for evolutionary biology, functional genomics, and systems biology analyses through KO-based functional profiles.

Methodology:

BlastKOALA applies a modified KOALA algorithm with BLAST searches against a curated non-redundant KEGG GENES-derived dataset organized by species, genus, and family, and maps assigned KOs onto KEGG pathways, BRITE hierarchies, and KEGG modules; GhostKOALA uses GHOSTX and incorporates Cd-hit clustered pangenome entries including viral genes.