Pandoomain

Pandoomain automates the acquisition, annotation, and analysis of genomic and protein domain context across large-scale bacterial genome datasets to reveal functional diversity and novel toxins.

Key Features:

• Automated Genome Acquisition: Retrieves genomes from NCBI.
• Protein Identification: Identifies proteins of interest using Hidden Markov Models (HMMs).
• Domain Annotation: Performs systematic protein domain annotation.
• Gene Neighborhood Analysis: Analyzes genomic context and gene neighborhoods.
• Scalable Workflow: Implements a Snakemake-based pipeline for high-throughput analysis across hundreds of thousands of genomes.

Scientific Applications:

• Domain Architecture Discovery: Reveals widespread domain architectural diversity, as demonstrated by the identification of 312 unique PT-TG domain architectures across 347,289 bacterial genomes.
• Novel Toxin Identification: Discovers new toxin families through genomic context analysis, including 24 new families of toxin domains associated with the W10XG trafficking domain variant.
• Functional Inference: Associates uncharacterized protein domains with specific biological systems, such as Type VI, Type VII, and CDI interbacterial antagonistic systems.
• Mobile Genetic Element Analysis: Identifies enrichment of mobile genetic elements near specific trafficking domains to reveal hotspots for genomic diversification.

Methodology:

Pandoomain is implemented as a Snakemake pipeline that automates genome acquisition from NCBI, protein identification using HMMs, domain annotation, and gene neighborhood analysis.