Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
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隆重推出 EzBioCloud：16S rRNA 基因序列和全基因组组件的分类学统一数据库。
DOI：
10.1099/ijsem.0.001755
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发表时间：
2017-05
影响因子：
2.8
通讯作者：
Chun J
中科院分区：
文献类型：
--
作者：
Yoon SH;Ha SM;Kwon S;Lim J;Kim Y;Seo H;Chun J
最近DNA测序技术的出现促进了基因组测序数据的使用，这些数据提供了用于细菌和细菌属成员的更信息化和精确的分类和鉴定的手段。由于目前的物种定义是基于一个给定的物种的类型和其他菌株之间的基因组序列的比较，建立一个正确的分类信息的基因组数据库是至关重要的需要，以加强我们的努力，探索原核生物多样性和发现新的物种，以及常规鉴定。在这里，我们介绍了一个集成的数据库，称为EzBioCloud，它拥有细菌和细菌的分类层次结构，由质量控制的16 S rRNA基因和基因组序列表示。筛选NCBI组装数据库中的全基因组组装的低质量，并进行复合鉴定生物信息学管道，其采用基于基因的搜索，然后计算平均核苷酸同一性。结果，该数据库由61 700个种/植物类型组成，其中包括13 132个有效公布的名称，以及62 362个在属、种和亚种水平上分类学鉴定的全基因组组装。 计算每个属或更高分类群的基因组特性，如基因组大小和DNA G+C含量，以及在人类微生物组数据中的出现率。这个统一的分类学数据库，16 S rRNA基因和基因组序列，伴随着生物信息学工具，应该加速基于基因组的分类和鉴定的细菌和细菌的成员。该数据库和相关搜索工具可在www.ezbiocloud.net/上查阅。
The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
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DOI：
10.1099/ijs.0.02963-0
发表时间：
2004-05-01
影响因子：
2.8
作者：
Thompson, CC;Thompson, FL;Swings, J
通讯作者：
Swings, J
DOI：
10.1093/bioinformatics/btv681
发表时间：
2016-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Richter M;Rosselló-Móra R;Oliver Glöckner F;Peplies J
通讯作者：
Peplies J
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
17.1
作者：
Snitkin ES;Zelazny AM;Thomas PJ;Stock F;NISC Comparative Sequencing Program Group;Henderson DK;Palmore TN;Segre JA
通讯作者：
Segre JA
影响因子：
9.8
作者：
Kyrpides NC;Hugenholtz P;Eisen JA;Woyke T;Göker M;Parker CT;Amann R;Beck BJ;Chain PS;Chun J;Colwell RR;Danchin A;Dawyndt P;Dedeurwaerdere T;DeLong EF;Detter JC;De Vos P;Donohue TJ;Dong XZ;Ehrlich DS;Fraser C;Gibbs R;Gilbert J;Gilna P;Glöckner FO;Jansson JK;Keasling JD;Knight R;Labeda D;Lapidus A;Lee JS;Li WJ;Ma J;Markowitz V;Moore ER;Morrison M;Meyer F;Nelson KE;Ohkuma M;Ouzounis CA;Pace N;Parkhill J;Qin N;Rossello-Mora R;Sikorski J;Smith D;Sogin M;Stevens R;Stingl U;Suzuki K;Taylor D;Tiedje JM;Tindall B;Wagner M;Weinstock G;Weissenbach J;White O;Wang J;Zhang L;Zhou YG;Field D;Whitman WB;Garrity GM;Klenk HP
通讯作者：
Klenk HP