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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics.

James T Monacell1, Ignazio Carbone

  • 1Center for Integrated Fungal Research, Department of Plant Pathology and Bioinformatics Research Center, North Carolina State University, NC 27695, USA.

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Summary

The SNAP Workbench now offers a web portal with over 189 bioinformatics tools for population genetics and genome analysis. This platform simplifies complex analyses and automates workflows for biological inference.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The stand-alone SNAP Workbench toolkit previously offered bioinformatics tools for phylogenetic and population genetic analyses.
  • A web-based portal front-end has now been developed using the Mobyle portal framework.

Purpose of the Study:

  • To provide a user-friendly web portal for accessing and executing a comprehensive suite of bioinformatics tools.
  • To expand the functionality beyond the original SNAP Workbench toolkit, incorporating new analysis types and a larger toolset.

Main Methods:

  • Development of a web portal using the Mobyle framework.
  • Integration of the SNAP Workbench toolkit's programs onto a high-performance Linux cluster.
  • Expansion of the tool selection to over 189 programs, including population genetics, genome assembly, metagenomics, and phylogenetic analysis tools.

Main Results:

  • The Mobyle SNAP Workbench web portal enables users to execute and manage complex command-line programs.
  • Users can launch multiple exploratory analyses and track the sequence of steps and parameters used.
  • Automated analysis pipelines for population genetics, metagenomics, and genome assembly facilitate data conversion, analysis, and visualization.

Conclusions:

  • The Mobyle SNAP Workbench web portal significantly enhances accessibility to advanced bioinformatics tools.
  • It supports complex, computationally intensive analyses and automates common workflows for biological inference.
  • The expanded toolset and user-friendly interface cater to a broader range of research needs in population genetics, genomics, and metagenomics.