RDP: Ribosomal Database Project

从基础和方法学的角度来看，核糖体RNA(RRNA)序列都是生物学的核心。作为细胞翻译过程中的关键要素，它们本身就值得进行详细的结构/功能研究。此外，它们的“进化特征”使它们在许多其他领域，特别是微生物学领域，成为非常有用的工具。对rRNA序列的比较分析(1)提供了rRNA本身的二级结构；(2)导致了宇宙生命树的推断--自然微生物分类的基础--以及古细菌的发现；(3)为新的和强大的微生物生态学方法提供了基础；(4)为医学诊断中的许多“探针”开发确定了目标；(5)为环境影响和生物修复评估提供了新的方法。所有这些研究都需要大量的rRNA数据，这些数据只有在适当的rRNA序列数据库的情况下才能有效地使用；一个不仅提供原始序列数据，而且将数据组织成比对的研究，提供系统发育概述，提供数据处理和分析的可用程序，并且(对许多用户)提供一套服务来帮助他们处理和分析数据。由于不存在如此有用、如此通用的rRNA序列数据库，因此在伊利诺伊大学建立了核糖体数据库项目(RDP)(由美国国家科学基金会资助)。通过其电子邮件和FTP服务器，RDP以各种用户选择的格式提供经过比对和系统发育排序的rRNA序列，以及用于处理和分析数据的各种软件。此外，还提供诸如自动序列比对、探针设计检查、用户选择的序列数据和系统发育树的子集以及rRNA二级结构等服务。这项提议的主要目标是：(1)提供RR NA数据的当前比对；(2)为这些数据提供系统发生树；(3)进一步使内部数据更新和数据管理程序自动化；(4)开发“下一代”序列比对编辑程序；(5)改进和扩大序列数据处理和分析工具，包括用于探针开发、序列比对和系统发生分析的工具；(6)增加新的和改进的RDP服务器软件和服务；(7)增加新形式的数据获取和分发；和()增加提供的核糖体相关序列比对的类型。鉴于目前的rRNA序列数据量(约2000个序列)和估计的未来水平(有些估计高达数百万)，RDP在未来的生物、医学和环境研究中发挥着至关重要的作用。

Ribosomal RNA (rRNA) sequences are central to biology from both the basic and the methodological perspectives. As the key elements in the cellular translation process they are worthy of detailed structure/function studies in their own right. In addition, their "evolutionary characteristics" make them extremely useful as tools in a number of other areas, microbiology in particular. Comparative analysis of rRNA sequences has (1) provided the secondary structure of the rRNAs themselves; (ii) led to the inference of the universal tree of life--a basis for a natural microbial classification--and the discovery of the Archaea; (iii) provided the basis for new and powerful approaches to microbial ecology; (iv) defined targets for much of the "probe" development in medical diagnosis; and (v) provided new methods for environmental impact and bioremediation assessment. All such studies require large amounts of rRNA data, and these can be used effectively only in the context of the appropriate database of rRNA sequences; one that not only provides the raw sequence data, but also organizes the data into alignments, provides a phylogenetic overview, makes available programs for data handling and analysis, and (for many users) offers a suite of services to assist them in their handling and analysis of the data. In that an rRNA sequence database this useful, this versatile, did not exist, the Ribosome Database Project (RDP) has been established at the University of Illinois (with a grant from NSF). Through its E-mail and FTP servers, the RDP offers aligned and phylogenetically ordered rRNA sequences in a variety of user-selected formats, as well as various software for handling and analysis of data. In addition, services such as automated sequence alignment, probe design checking, user-selected subsets of the sequence data and phylogenetic trees, and rRNA secondary structures are provided. Major objectives of this proposal are: (i) provide current alignments of rR NA data; (ii) provide a phylogenetic tree for those data; (iii) further automate the internal data updating and data management procedures; (iv) develop a "next generation" sequence alignment editor; (v) improve and expand the sequence data handling and analysis tools, including those for probe development, sequence alignment, and phylogenetic analysis; (vi) add new and improved software and services to the RDP servers; (vii) add new forms of data access and distribution; and (viii) increase the types of ribosome-related sequence alignments offered. Given the present volume of rRNA sequence data (approximately 2000 sequences) and the estimated future level (some estimates running into the millions), the RDP has an essential role to play in biological, medical and environmental research in the future.