GeneScanner: profiling genetic variation across bacterial populations.

Area of Science:

• Microbial Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Genome sequencing advances microbiology, linking genetic and phenotypic variation.
• Functional screens and comparative genomics reveal trait mechanisms and diversity.
• Integrating these approaches is challenging due to bioinformatics skill gaps.

Purpose of the Study:

• To develop GeneScanner, a user-friendly tool for analyzing gene and protein variation in bacterial genomes.
• To enable researchers to interpret microbial variation and its link to phenotypes.
• To bridge the skills gap in bioinformatics for microbial genomics research.

Main Methods:

• GeneScanner detects genetic variants and amino acid substitutions in homologous sequences.
• Utilized synthetic data and three empirical case studies for validation.
• Applied to diverse bacterial species and phenotypes.

Main Results:

• GeneScanner reliably identifies nucleotide and protein-level variants associated with specific traits.
• Demonstrated accuracy using synthetic and real-world data.
• Case studies highlight broad applicability across different microbial systems.

Conclusions:

• GeneScanner enhances the functional interpretation of microbial variation.
• The tool supports research in antimicrobial resistance, host-pathogen interactions, and microbial evolution.
• Facilitates broader research in epidemiology and public health by simplifying genomic analysis.