The Ribosomal Database Project: Automation, Integration and Education

通过对核糖体RNA序列的比较分析，我们对地球上生命形式之间进化关系的看法发生了革命性的变化。现在，生命被认为属于三种主要的进化谱系之一：真核生物、细菌或真核生物。这种范式的转变不仅挑战了对生命起源的杜尔沉闷的理解，而且为研究现存生命--特别是微生物的巨大多样性--提供了一个知识框架。核糖体数据库计划（RDP）的核心是核糖体RNA序列库，它使生物学取得了重大进展。RDP是一个增值数据库，通过RDP网站提供给研究界。RDP将原始序列组织成比对，注释rRNA序列数据，提供生命的系统发育概述，并提供一套服务和工具来帮助处理和分析数据。这些RDP产品广泛应用于分子生物学和进化生物学、微生物生态学、细菌鉴定、表征微生物种群以及了解生命的多样性。自动化序列采集、比对和注释程序，使RDP能够提供高质量的最新数据2.提供新的和增强的系统发育和生态工具，沿着升级的网站，以允许我们的用户利用这些数据并分析他们自己的数据。和3.为用户社区提供培训、教育和支持，并协助传播在系统发育和生态研究中使用rRNA数据的“最佳做法”。最近在二级结构感知rRNA自动比对方面的突破使这些目标得以实现。

Our view of the evolutionary relationships among life forms on Earth was revolutionized by the comparative analysis of ribosomal RNA sequences. Life is now viewed as belonging to one of three primary lines of evolutionary descent: the Archaea, Bacteria or Eucarya. This shift in paradigm has not only challenged dour understanding of life's origin, but also provided an intellectual framework for studying extant life - particularly the vast diversity of microorganisms. The repository of rRNA sequences that has permitted major advances in biology form the core of the Ribosomal Database Project (RDP). RDP is a value added database available to the research community through the RDP website. The RDP organized raw sequences into alignments, annotates rRNA sequence data, provides a phylogenetic overview of life and offers a suite of services and tools to assist in the handling and analysis of the data. These RDP products are widely used in molecular phylogeny and evolutionary biology, microbial ecology, bacterial identification, characterizing microbial populations, and in understanding the diversity of life.The RDP will provide 1. Automation of sequence harvesting, alignment and annotation procedures to allow the RDP to provide high-quality up-to-date data 2. Provision of new and enhanced phylogeny and ecology tools, along with an upgraded website, to allow our users to make use of these date and to analyze their own data. And 3. Provision of training, education, and support to the user community and assistance in the dissemination 'best practices' for the use of rRNA data in phylogenetic and ecological studies. Recent breakthroughs in secondary-structure aware rRNA autoaligners have made these goals achievable.