Karp Peter D, Ivanova Natalia, Krummenacker Markus, Kyrpides Nikos, Latendresse Mario, Midford Peter, Ong Wai Kit, Paley Suzanne, Seshadri Rekha
Bioinformatics Research Group, SRI International, Menlo Park, CA, United States.
DOE Joint Genome Institute, Walnut Creek, CA, United States.
Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019.
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.
微生物基因组网络门户具备广泛的功能，可满足科学家在信息查找和分析方面的诸多需求。本文比较了主要微生物基因组网络门户的功能，以帮助研究人员确定最适合其需求的门户。我们评估了BioCyc、KEGG、Ensembl Bacteria、KBase、IMG和PATRIC的生物信息学工具和数据内容。对于每个门户，我们的评估比较并统计了可用功能。BioCyc的优势包括其基因组和代谢工具、多搜索功能、基于表格的分析工具、调控网络工具和数据、组学数据分析工具、数据内容的广度以及大量经过整理的数据。KEGG的优势包括其基因组和代谢工具。Ensembl Bacteria的优势包括其基因组工具和大量基因组。KBase的优势包括其基因组工具和代谢模型。IMG的优势包括其基因组工具、多搜索功能、大量基因组、基于表格的分析工具以及数据内容的广度。PATRIC的优势包括其大量基因组、基于表格的分析工具、代谢模型以及数据内容的广度。
