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Review
. 2019 Feb 22:10:208.
doi: 10.3389/fmicb.2019.00208. eCollection 2019.

A Comparison of Microbial Genome Web Portals

Peter D Karp  1 , Natalia Ivanova  2 , Markus Krummenacker  1 , Nikos Kyrpides  2 , Mario Latendresse  1 , Peter Midford  1 , Wai Kit Ong  1 , Suzanne Paley  1 , Rekha Seshadri  2
Affiliations
Review

A Comparison of Microbial Genome Web Portals

Peter D Karp et al. Front Microbiol. .

Abstract

Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs. We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. For each portal, our assessment compared and tallied the available capabilities. The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content, and large amount of curated data. The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes. The strengths of KBase include its genomic tools and metabolic models. The strengths of IMG include its genomic tools, multi-search capabilities, large number of genomes, table-based analysis tools, and breadth of data content. The strengths of PATRIC include its large number of genomes, table-based analysis tools, metabolic models, and breadth of data content.

Keywords: genome databases; genome portals; microbial genome databases; microbial genomes; microbial genomics.

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Figures

Figure 1
Figure 1
Spider plot of the data in Table 11, excluding the Multi-Search row to enhance resolution.
See this image and copyright information in PMC

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