micropan

micropan performs pan-genome analysis in R by identifying and characterizing gene families across multiple prokaryotic strains to quantify species-level genetic diversity.

Key Features:

• Comprehensive pan-genome analysis: Identifies and analyzes gene families across multiple prokaryotic strains to explore species genetic diversity.
• Integration with R: Leverages R for statistical analysis and graphical capabilities during pan-genome investigations.
• Computational efficiency: Integrates external free software for computationally intensive tasks to process large genomic datasets.
• Pipeline construction: Provides functions to build customized computational pipelines for pan-genome analyses.

Scientific Applications:

• Species diversity exploration: Analyzes pan-genomes to assess genetic diversity within a species and identify unique gene families.
• Functional gene identification: Aids in pinpointing gene families relevant to bacterial survival and strain differentiation.
• Example dataset analysis: Applicable to analyses of Enterococcus faecalis pan-genome datasets (a gram-positive bacterium).

Methodology:

Compiles unique gene families from multiple strains and processes these datasets using R and integrated external computational tools to reveal patterns in microbial diversity and gene content.