Maidak B L, Cole J R, Parker C T, Garrity G M, Larsen N, Li B, Lilburn T G, McCaughey M J, Olsen G J, Overbeek R, Pramanik S, Schmidt T M, Tiedje J M, Woese C R
Department of Microbiology, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA.
Nucleic Acids Res. 1999 Jan 1;27(1):171-3. doi: 10.1093/nar/27.1.171.
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
核糖体数据库项目（RDP-II），先前由迈达克等人描述过[《核酸研究》（1997年），25卷，第109 - 111页]，现在由密歇根州立大学微生物生态中心托管。RDP-II是一个经过整理的数据库，以比对和未比对的形式提供核糖体RNA（rRNA）核苷酸序列数据、分析服务及相关计算机程序。在过去两年中，数据比对已更新，现在包含超过9700个小亚基rRNA序列。ObjectStore数据库的最新开发将实现数据的更快速更新、更高的数据准确性并增加用户访问权限。RDP-II包括rRNA序列的系统发育有序比对、推导的系统发育树、rRNA二级结构图以及用于处理、分析和显示比对及树的各种软件程序。数据可通过匿名ftp（ftp.cme.msu.edu）和万维网（http://www.cme.msu.edu/RDP）获取。万维网服务器提供核糖体探针检查、用户提交序列的近似系统发育定位、可能的嵌合rRNA序列筛选、自动比对以及将未知序列在现有系统发育树上的建议定位。RDP-II还有其他实用工具，包括距离矩阵、末端限制性片段长度多态性分析（T-RFLP）以及一个基于Java的系统发育树查看器，可用于创建子树。
