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PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

Sandip Paul1, Archana Bhardwaj2, Sumit K Bag2

  • 1Department of Microbiology, University of Washington, Seattle, WA 98195 USA.

Genomics
|October 13, 2015
PubMed
Summary
This summary is machine-generated.

PanCoreGen is a new tool for microbial genomics, analyzing the pan-genome to understand evolution and virulence. It aids in annotating genomes and identifying genes, offering insights into pathogen evolution.

Keywords:
Core-genomeDraft-genome annotationPan-genomeProtein-coding genes

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Area of Science:

  • Microbial Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Genomic data analysis is crucial for understanding microbial evolution.
  • Pan-genome analysis reveals the complete genetic repertoire of a species.
  • Evolution of virulence is a key area of interest in microbial genomics.

Purpose of the Study:

  • Introduce PanCoreGen, a novel application for microbial pan- and core-genomic profiling.
  • Address limitations of existing pan-genomic analysis tools.
  • Provide an integrated annotation structure for species-specific pan-genomic profiles.

Main Methods:

  • PanCoreGen analyzes microbial protein-coding genes.
  • The tool integrates annotation and structure for pan-genomic profiles.
  • It supports annotation of draft genomes/contigs and detection of unidentified genes.

Main Results:

  • PanCoreGen overcomes limitations of current pan-genomic tools.
  • The application generates user-defined group-specific datasets.
  • Analysis of Salmonella genomes revealed adaptive convergence of horizontally transferred genes in pathogenic serovars.

Conclusions:

  • PanCoreGen is a state-of-the-art tool for microbial phylogenomics and pathogenomics.
  • The tool facilitates a deeper understanding of microbial evolution and virulence.
  • It aids in the identification of adaptive evolutionary footprints in microbial pathogens.