ExplorePipolin

ExplorePipolin identifies, reconstructs, and annotates pipolins in draft, contig-based bacterial genomes to enable analysis of mobile genetic elements and their role in antimicrobial resistance.

Key Features:

• Implementation: Python-based bioinformatics pipeline for automated processing of bacterial genome assemblies.
• Screening and Reconstruction: Screens draft, contig-based bacterial genomes to identify pipolins and reconstructs their structure by piecing together contigs when necessary.
• Annotation Capabilities: Annotates pipolin boundaries and encoded genes using a custom database tailored for pipolin elements.
• Pipolin Characterization: Focuses on MGEs characterized by integrative and plasmidic nature and the presence of a primer-independent DNA polymerase.
• Output Formats: Produces standard file formats suitable for downstream comparative genomics analyses.

Scientific Applications:

• Pipolin detection and structural analysis: Identification and reconstruction of pipolin architectures from fragmented draft genomes.
• Comparative genomics of MGEs: Generation of annotated datasets for comparative analyses of mobile genetic elements across bacterial isolates.
• Antimicrobial resistance research: Investigation of the contribution of pipolins to the spread and evolution of antimicrobial resistance genes.

Methodology:

Implemented in Python; screens contig-based draft bacterial genomes, reconstructs pipolins by piecing together contigs, annotates boundaries and genes using a custom pipolin database, and exports results in standard comparative-genomics file formats.