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A Comparison of Microbial Genome Web Portals.

Peter D Karp1, Natalia Ivanova2, Markus Krummenacker1

  • 1Bioinformatics Research Group, SRI International, Menlo Park, CA, United States.

Frontiers in Microbiology
|March 12, 2019
PubMed
Summary

This study compares microbial genome web portals, evaluating bioinformatics tools and data content. BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC offer diverse strengths for microbial genomics research.

Keywords:
genome databasesgenome portalsmicrobial genome databasesmicrobial genomesmicrobial genomics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Microbial genome web portals are essential resources for scientists.
  • These platforms offer diverse capabilities for information retrieval and data analysis.
  • Selecting the appropriate portal is crucial for efficient research.

Purpose of the Study:

  • To compare the capabilities of major microbial genome web portals.
  • To assist researchers in identifying the best-suited portal(s) for their specific needs.
  • To provide a comprehensive assessment of bioinformatics tools and data content.

Main Methods:

  • Evaluated six prominent microbial genome web portals: BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC.
  • Assessed the bioinformatics tools and data content offered by each portal.
  • Compared and tallied the available capabilities for each platform.

Main Results:

  • BioCyc excels in genomic, metabolic, and regulatory tools, multi-search, omics analysis, and curated data breadth.
  • KEGG and Ensembl Bacteria offer strong genomic and metabolic tools, with Ensembl Bacteria hosting a large genome collection.
  • KBase provides robust genomic tools and metabolic models.
  • IMG and PATRIC feature extensive genomic tools, multi-search (IMG), table-based analysis, large genome collections (IMG, PATRIC), and broad data content.

Conclusions:

  • Each microbial genome web portal possesses distinct strengths.
  • Researchers can leverage this comparative analysis to choose platforms aligning with their specific genomic and metabolic research requirements.
  • The selection depends on the need for specific tools, data types, and analytical functionalities.