GhostKOALA

GhostKOALA assigns KEGG Orthology (KO) terms to metagenome sequences to characterize gene functions and enable reconstruction of KEGG pathways, BRITE hierarchies, and KEGG modules.

Key Features:

• KO assignment: Assigns KEGG Orthology (KO) terms to metagenomic sequences for gene-level functional annotation.
• GHOSTX search algorithm: Performs rapid sequence searches using GHOSTX optimized for handling large metagenomic datasets.
• Augmented reference dataset: Utilizes an augmented reference that includes Cd-hit clusters and viral genes to broaden annotation scope beyond non-redundant pangenome sequences.
• Contrast to BlastKOALA: Uses GHOSTX rather than BLAST and incorporates additional Cd-hit clustered sequences including viral genes compared with BlastKOALA's BLAST-based approach.
• Pathway and hierarchy reconstruction: Generates KO-based reconstructions of KEGG pathways, BRITE hierarchies, and KEGG modules for high-level functional inference.
• Downstream compatibility: Produces result files suitable for use with KEGG Mapper for comparative pathway and functional analyses.

Scientific Applications:

• Metagenome annotation: Annotating metagenomic datasets by assigning KO terms to sequence data.
• Gene function characterization: Characterizing individual gene functions through KEGG Orthology assignments.
• Functional and ecological inference: Inferring functional potential and ecological roles of microbial communities via KO-based pathway reconstructions.
• Comparative pathway analysis: Enabling comparative analyses of metabolic and functional diversity across metagenomic datasets using KEGG pathway reconstructions.
• Environmental microbiology, ecology, and systems biology: Supporting studies in environmental microbiology, ecology, and systems biology by providing functional profiles mapped to KEGG modules and BRITE hierarchies.

Methodology:

Performs sequence searches with GHOSTX against KEGG orthology references (including Cd-hit clusters with viral genes) to assign KO terms, which are used to reconstruct KEGG pathways, BRITE hierarchies, and KEGG modules.