AlbaTraDIS

AlbaTraDIS performs large-scale comparative analysis of Transposon Directed Insertion-site Sequencing (TraDIS) experiments to identify genes influencing bacterial survival under environmental stresses such as antimicrobial exposure.

Key Features:

• Comparative Analysis: Compares multiple TraDIS datasets simultaneously to identify common genetic responses across experimental conditions.
• Impact Prediction: Predicts the impact of transposon insertions on nearby genes to infer disruptions of gene expression and function.
• Statistical Analysis: Applies statistical methods from the Bio-TraDIS toolkit to identify significant genetic elements involved in phenotypes.
• Data Visualization: Produces visualizations to explore patterns and interpret TraDIS results.
• Experimental Validation Support: Generates filtered lists of candidate genes implicated in specific phenotypes to guide experimental validation.

Scientific Applications:

• Bacterial stress survival studies: Used to dissect genetic determinants of bacterial survival and adaptation under environmental stresses and antimicrobial exposure.
• Triclosan resistance in Escherichia coli: Applied to identify genes involved in E. coli resistance to the biocide Triclosan, confirming known loci such as fabI and highlighting novel candidate loci with experimental validation.

Methodology:

Integrates and analyzes large-scale TraDIS datasets, predicts impacts of transposon insertions on nearby genes, and applies statistical methods from the Bio-TraDIS toolkit; implemented in Python 3.