KEGG_Extractor

KEGG_Extractor extracts and classifies gene sequences from the KEGG Orthology (KO) database to enable functional annotation and pathway analysis of microbial genomes.

Key Features:

• Efficient extraction: Uses an iterative keyword matching algorithm to precisely extract and classify amino acid and nucleotide sequences from KEGG annotation outputs.
• Species-specific analysis: Enables targeted extraction of gene sequences for particular organisms or taxonomic groups within microbial datasets.
• High-performance processing: Implements a computational approach optimized for rapid extraction and classification of KO-based annotations.

Scientific Applications:

• Functional annotation: Links genes to KEGG pathways to support reconstruction of molecular networks and pathway-level interpretation.
• Pathway analysis: Applied to analyze the Wood–Ljungdahl (WL) pathway, identifying approximately 226 archaeal strains with WL pathway-related genes, including Methanococcus maripaludis, Methanosarcina mazei, and members of Methanobacterium, Thermococcus, and Methanosarcina.
• Database construction: Facilitated creation of the ARWL database, reported as comprehensive and high accuracy for WL-related gene collections.

Methodology:

Iterative keyword matching of KEGG annotation records to extract and classify amino acid and nucleotide gene sequences.