25 years of serving the community with ribosomal RNA gene reference databases and tools
25 years of serving the community with ribosomal RNA gene reference databases and tools
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DOI：
10.1016/j.jbiotec.2017.06.1198
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发表时间：
2017-11-10
影响因子：
4.1
通讯作者：
Ludwig, Wolfgang
中科院分区：
文献类型：
--
作者：
Gloeckner, Frank Oliver;Yilmaz, Pelin;Ludwig, Wolfgang
席尔瓦(lat。是一个综合性的网络资源，提供来自细菌、古生菌和真核生物领域的核糖体RNA基因（rDNA）序列的最新、高质量数据集。SILVA的历史可以追溯到1991年，当时慕尼黑工业大学的Wolfgang Ludwig博士开始了集成软件工作台ARB（后期）。树)，以支持基于SSU和LSU rDNA标记基因的高质量系统发育推断和分类。当时，ARB项目既维护了序列参考数据集，也维护了数据分析软件包。2005年，随着DNA序列数据的大量增加，软件系统ARB和相应的rRNA数据库SILVA的维护工作被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分开。ARB一直在不断开发，以包含新特性并改进工作台的可用性。世界各地成千上万的用户都喜欢在中央图形用户界面下无缝集成通用分析工具，并结合其多功能性。第一个SILVA版本于2007年2月部署，基于EMBL-EBI/ENA版本89。从那时起，提供各种风格的数据库内容的完整SILVA版本至少每年发布一次，并辅以中间网络版本，其中仅更新SILVA网络数据集。SILVA是世界上唯一一个特别强调未栽培（环境）序列分支的一致命名的rDNA数据库项目，其中没有有效描述的栽培代表可用。此外，SILVA还专门维护全面对齐的16S/18S rDNA和23S/28S rDNA序列数据集。此外，SILVA序列和树被设计为包括真核生物，这是rDNA数据库的另一个独特特征。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、医学诊断到学术界和工业界的生物技术和质量控制。
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.