A Comparison of Microbial Genome Web Portals

Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus; Kyrpides, Nikos; Latendresse, Mario; Midford, Peter; Ong, Wai Kit; Paley, Suzanne; Seshadri, Rekha

doi:10.3389/fmicb.2019.00208

Title: A Comparison of Microbial Genome Web Portals

Journal Article · 22 February 2019 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.00208 · OSTI ID:1559174

Karp, Peter D. ^[1]; Ivanova, Natalia ^[2]; Krummenacker, Markus ^[1]; Kyrpides, Nikos ^[2]; Latendresse, Mario ^[1]; Midford, Peter ^[1]; Ong, Wai Kit ^[1]; Paley, Suzanne ^[1]; Seshadri, Rekha ^[2]

SRI International, Menlo Park, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Climate and Environmental Sciences Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1559174

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Journal Issue: FEB Vol. 10; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (24)

Evidence for an association of interferon gene variants with sudden infant death syndrome Hafke, Angelina; Schürmann, Peter; Rothämel, Thomas International Journal of Legal Medicine, Vol. 133, Issue 3 https://doi.org/10.1007/s00414-018-1974-6	journal	January 2019
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
The BioCyc collection of microbial genomes and metabolic pathways Karp, Peter D.; Billington, Richard; Caspi, Ron Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx085	journal	August 2017
MicrobesOnline: an integrated portal for comparative and functional genomics Dehal, P. S.; Joachimiak, M. P.; Price, M. N. Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400 https://doi.org/10.1093/nar/gkp919	journal	November 2009
PATRIC, the bacterial bioinformatics database and analysis resource Wattam, Alice R.; Abraham, David; Dalay, Oral Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1099	journal	November 2013
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1101	journal	November 2016
IMG/M: integrated genome and metagenome comparative data analysis system Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw929	journal	October 2016
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species Kersey, Paul Julian; Allen, James E.; Allot, Alexis Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1011	journal	October 2017
The Omics Dashboard for interactive exploration of gene-expression data Paley, Suzanne; Parker, Karen; Spaulding, Aaron Nucleic Acids Research, Vol. 45, Issue 21 https://doi.org/10.1093/nar/gkx910	journal	October 2017
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
The BioCyc collection of microbial genomes and metabolic pathways Karp, Peter D.; Billington, Richard; Caspi, Ron Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx085	journal	August 2017
MicrobesOnline: an integrated portal for comparative and functional genomics Dehal, P. S.; Joachimiak, M. P.; Price, M. N. Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400 https://doi.org/10.1093/nar/gkp919	journal	November 2009
PATRIC, the bacterial bioinformatics database and analysis resource Wattam, Alice R.; Abraham, David; Dalay, Oral Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1099	journal	November 2013
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1101	journal	November 2016
IMG/M: integrated genome and metagenome comparative data analysis system Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw929	journal	October 2016
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species Kersey, Paul Julian; Allen, James E.; Allot, Alexis Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1011	journal	October 2017
The Omics Dashboard for interactive exploration of gene-expression data Paley, Suzanne; Parker, Karen; Spaulding, Aaron Nucleic Acids Research, Vol. 45, Issue 21 https://doi.org/10.1093/nar/gkx910	journal	October 2017
The MetaCyc database of metabolic pathways and enzymes Caspi, Ron; Billington, Richard; Fulcher, Carol A. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx935	journal	October 2017

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Current Status and Potential Applications of Underexplored Prokaryotes Goh, Kian Mau; Shahar, Saleha; Chan, Kok-Gan Microorganisms, Vol. 7, Issue 10 https://doi.org/10.3390/microorganisms7100468	journal	October 2019
PHI-base: the pathogen–host interactions database Urban, Martin; Cuzick, Alayne; Seager, James Nucleic Acids Research https://doi.org/10.1093/nar/gkz904	journal	November 2019
PHI-base: the pathogen-host interactions database. Urban, Martin; Cuzick, Alayne; Seager, James Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.44805	text	January 2020
Current Status and Potential Applications of Underexplored Prokaryotes Goh, Kian Mau; Shahar, Saleha; Chan, Kok-Gan Microorganisms, Vol. 7, Issue 10 https://doi.org/10.3390/microorganisms7100468	journal	October 2019

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