HattCI

HattCI identifies attC sites in genomic and metagenomic DNA to characterize integrons and study integron-mediated horizontal gene transfer associated with antibiotic resistance.

Key Features:

• Generalized Hidden Markov Model: Employs a generalized hidden Markov model to probabilistically describe each core component of an attC site, modeling the 55 to 141-nucleotide imperfect inverted repeats that characterize attC sites.
• High sensitivity and validation: Achieved sensitivity up to 91.9% in twofold cross-validation on a manually curated reference dataset of 231 attC sites from class 1 and 2 integrons while maintaining satisfactory false-positive rates.
• Metagenomic application: Identified significantly higher numbers of attC sites when applied to metagenomic datasets from 35 microbial communities, particularly in samples enriched for horizontally transferred elements.

Scientific Applications:

• Integron and resistance gene studies: Enables identification of attC sites to study integron-mediated horizontal gene transfer and the distribution and evolution of antibiotic resistance genes.
• Microbial community and mobility surveys: Facilitates detection of attC sites in metagenomic datasets to assess prevalence and dynamics of mobile gene cassettes across diverse environments.

Methodology:

Uses a generalized hidden Markov model that probabilistically models attC core components and 55–141 nt imperfect inverted repeats; validated by twofold cross-validation on a curated set of 231 attC sites from class 1 and 2 integrons and applied to metagenomic datasets from 35 microbial communities.