KAAS

KAAS assigns KEGG Orthology (KO) identifiers (K numbers) to genes and maps them to KEGG pathway maps and BRITE functional hierarchies for functional annotation and pathway reconstruction of complete and draft genomes.

Key Features:

• K number assignment: Assigns KEGG Orthology (KO) identifiers (K numbers) to genes based on sequence similarity.
• Bi-directional best hit and heuristics: Utilizes bi-directional best hit information combined with heuristic approaches to determine ortholog relationships.
• BLAST comparisons: Performs BLAST comparisons against the curated KEGG GENES database.
• Smith-Waterman scoring: Calculates Smith-Waterman scores for best-hit information to refine ortholog assignments.
• Pathway and BRITE reconstruction: Automatically generates and reconstructs KEGG pathway maps and BRITE functional hierarchies from assigned K numbers.
• Alignment to curated database: Produces assignments aligned closely with the manually curated KEGG GENES database.

Scientific Applications:

• Functional annotation of genomes: Provides KO-based functional annotations for complete and draft genomes.
• Pathway mapping and reconstruction: Enables reconstruction and mapping of metabolic and signaling pathways via KEGG pathway maps.
• Systems biology: Supports systems-level analyses by linking genes to pathway and BRITE hierarchies.
• Metabolic engineering: Facilitates identification of pathway components relevant to metabolic engineering.
• Comparative genomics: Enables comparison of gene functions and pathways across genomes using KO assignments.

Methodology:

Performs BLAST comparisons against the KEGG GENES database, computes Smith-Waterman scores, applies bi-directional best hit information and heuristic approaches to assign KO identifiers, and generates KEGG pathway maps and BRITE hierarchies from assigned K numbers.