The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.
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DOI：
10.1093/nar/gky467
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发表时间：
2018-07-02
影响因子：
14.9
通讯作者：
Konstantinidis KT
中科院分区：
文献类型：
--
作者：
Rodriguez-R LM;Gunturu S;Harvey WT;Rosselló-Mora R;Tiedje JM;Cole JR;Konstantinidis KT
小亚基核糖体RNA基因（16SrRNA）已被成功地用于原核生物物种和群落多样性的分类和研究，但它在物种和更精细水平上的分辨率有限，不能代表整个基因组的多样性和流动性。为了克服这些局限性，我们引入了微生物基因组图谱（MiGA），这是一个网络服务器，允许对未知的查询基因组序列进行分类，完整或部分，对所有分类学分类的类群与可用的基因组序列，以及与其他相关基因组的比较，包括未培养的，基于基因组聚合平均核苷酸和氨基酸同一性（ANI/AAI）的概念。MiGA集成了序列质量修剪和组装的最佳实践，并允许输入来自分离基因组、单细胞序列和宏基因组组装基因组（MAG）的原始读数或组装。此外，MiGA可以将相同或密切相关物种的数百个密切相关的基因组作为输入（所谓的"进化枝项目"），以评估它们的基因内容多样性和进化关系，并计算重要的进化枝属性，如泛基因组和核心基因组。因此，MiGA有望促进一系列基于基因组的分类学和多样性研究，以及环境和临床环境的质量评估。MiGA可在www.example.com上获得。
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called ‘Clade Project’) to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.
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影响因子：
2.7
作者：
Garrison NL;Rodriguez J;Agnarsson I;Coddington JA;Griswold CE;Hamilton CA;Hedin M;Kocot KM;Ledford JM;Bond JE
通讯作者：
Bond JE
影响因子：
14.9
作者：
Cochrane G;Karsch-Mizrachi I;Takagi T;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
DOI：
10.1073/pnas.0409727102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
4.4
作者：
Rodriguez-R, Luis M.;Castro, Juan C.;Konstantinidis, Konstantinos T.
通讯作者：
Konstantinidis, Konstantinos T.
影响因子：
3.2
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM