BtToxin_Digger

BtToxin_Digger mines toxin protein genes from Bacillus thuringiensis and related genomic and metagenomic datasets to identify cry genes and other insecticidal or virulence factors for downstream analysis.

Key Features:

• High-throughput mining: Processes large-scale genomic and metagenomic datasets for systematic toxin gene discovery.
• BLAST-based alignment: Uses BLAST for sequence alignment and identification of homologous sequences.
• HMM detection: Employs Hidden Markov Models to detect protein families and domains relevant to toxin proteins.
• SVM classification: Applies Support Vector Machines to classify candidate sequences based on patterns from known toxin genes.
• Target extensibility: Allows incorporation of additional query sequences to identify non-Bt target genes.
• Toxin and virulence identification: Identifies major toxin genes including cry genes and potential novel virulence factors.
• Outputs for downstream analysis: Produces results intended to support downstream analyses and experimental design.

Scientific Applications:

• GM crop development: Supporting discovery and characterization of cry genes for genetically modified crop pest resistance.
• Microbial pest control research: Informing exploration and development of microbial pesticide agents and pest management strategies.
• Metagenomic screening: Detecting Bt toxin genes in environmental and metagenomic samples.
• Novel toxin discovery: Identifying candidate insecticidal and virulence factors for experimental validation.

Methodology:

Integrates BLAST for sequence alignment, HMMs for protein family and domain detection, and SVMs for classification to mine toxin genes from large-scale genomic and metagenomic data.