Integron Finder

Integron Finder detects and characterizes integrons and related genetic elements in DNA sequences to identify attC sites, integron-integrases, gene cassettes, and structural features relevant to bacterial adaptation and the spread of antibiotic resistance.

Key Features:

• Detection Capabilities: Identifies integrons, integron-integrases lacking attC sites, and clusters of attC sites without neighboring integron-integrases.
• Covariance models for attC: Uses covariance models to search for and detect attC sites.
• HMM profiles for integron-integrases: Employs Hidden Markov Model (HMM) profiles to identify integron-integrases.
• Pattern matching for regulatory sites: Utilizes pattern matching to detect promoters and the attI recombination site.
• attC similarity and cassette analysis: Analyzes similarity between attC sites and detects novel cassette pools not present in existing databases.

Scientific Applications:

• Genomic Analysis: Applied to bacterial genomes of intermediate size to map integron distribution and investigate the absence of integrons in phyla such as α-Proteobacteria.
• Evolutionary Insights: Analyzes attC similarity and cassette composition to infer integron evolution, steps of gene acquisition, and stabilization within genomes.
• Antibiotic Resistance: Identifies integrons and associated gene cassettes to study mechanisms underlying the spread of antibiotic resistance.
• Regulatory Networks: Informs studies of promoters and regulatory elements controlling integron expression and their modulation by environmental signals and host physiology.

Methodology:

Covariance models to search for attC sites, Hidden Markov Model (HMM) profiles to identify integron-integrases, and pattern matching to detect promoters and the attI site; searches are performed on bacterial genome sequences to identify integrons, integron-integrases lacking attC sites, and clusters of attC sites without neighboring integrases.