Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, Germany; Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
J Biotechnol. 2017 Nov 10;261:169-176. doi: 10.1016/j.jbiotec.2017.06.1198. Epub 2017 Jun 23.
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.
Silva（拉丁语：森林）是一个综合性的网络资源，提供最新的高质量细菌、古菌和真核生物领域核糖体 RNA 基因（rDNA）序列比对数据集相关的服务。Silva 可以追溯到 1991 年，当时慕尼黑工业大学的 Wolfgang Ludwig 博士开始开发集成软件工作平台 ARB（拉丁语：树），以支持基于小亚基和大亚基 rDNA 标记基因的高质量系统发育推断和分类学。当时，ARB 项目既维护序列参考数据集，也维护数据分析软件包。2005 年，随着 DNA 序列数据的大量增加，ARB 软件系统和相应的 rRNA 数据库 Silva 的维护工作在慕尼黑和不来梅的微生物基因组学和生物信息学研究小组之间进行了分工。ARB 不断发展，增加了新的功能，提高了工作平台的可用性。全球数以千计的用户赞赏其在中央图形用户界面下无缝集成通用分析工具的功能，以及其多功能性。2007 年 2 月，基于 EMBL-EBI/ENA 发布的 89 版，首次部署了 Silva。从那时起，每年至少发布一次包含各种风味数据库内容的完整 Silva 版本，并通过仅更新 Silva 网络数据集的中间网络版本进行补充。Silva 是全球唯一专门强调对未培养（环境）序列的进化枝进行一致命名的 rDNA 数据库项目，对于那些没有有效描述的培养代表的序列尤其如此。Silva 还维护全面对齐的 16S/18S rDNA 和 23S/28S rDNA 序列数据集，这是其独有的特色。此外，Silva 对齐和树的设计包含了真核生物，这是 rDNA 数据库中的另一个独特特征。随着 2007 年欧洲核糖体 RNA 数据库项目的终止，Silva 数据库已成为欧洲权威的 rDNA 数据库项目。ARB 和 Silva 的应用范围从生物多样性分析、医学诊断到生物技术和质量控制，涵盖学术界和工业界。
