CryProcessor

CryProcessor identifies and extracts three-domain Cry (3d-Cry) toxins from Illumina sequencing data and protein FASTA files to enable analysis of Bacillus thuringiensis pesticidal proteins.

Key Features:

• HMM-based scanning: Uses HMM-based scanning to detect candidate Cry toxin sequences.
• Domain layout prediction: Predicts domain layout within arbitrary sequences to determine precise domain boundaries.
• Three-domain extraction: Extracts Cry toxin sequences that contain exactly three domains.
• Domain sequence retrieval: Retrieves specific domain sequences from identified Cry proteins.
• Assembly graph search: Searches directly within assembly graphs to analyze raw Illumina sequencing data and address fragmented assemblies.
• Bt nomenclature comparison: Compares identified toxins against established Bacillus thuringiensis (Bt) nomenclature.
• Large-dataset efficiency: Operates efficiently on large datasets across multiple operational modes.
• Input formats: Accepts Illumina sequence data and protein FASTA files as inputs.
• Extended domain extraction: Enables extraction of domain sequences beyond limitations reported for prior tools (e.g., CryGetter).

Scientific Applications:

• Novel toxin discovery: Large-scale screening for novel 3d-Cry toxins from sequencing datasets.
• Resistance monitoring: Supports investigation of emerging resistance to known insecticidal toxins.
• In silico toxin design: Facilitates retrieval of domain sequences to support in silico construction of artificial toxins.
• Bioinsecticide research: Supports characterization of Bt-derived insecticidal proteins for bioinsecticide development and sustainable agriculture research.

Methodology:

HMM-based scanning, retrieval of domain information, prediction of domain layout in arbitrary sequences, extraction of sequences containing exactly three domains, comparison against Bt nomenclature, and searching within assembly graphs.