A new version of the RDP (Ribosomal Database Project)
A new version of the RDP (Ribosomal Database Project)
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DOI：
10.1093/nar/27.1.171
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发表时间：
1999-01-01
影响因子：
14.9
通讯作者：
Woese, CR
中科院分区：
文献类型：
--
作者：
Maidak, BL;Cole, JR;Woese, CR
核糖体数据库项目（RDP-II），先前由Maidak等人描述[核酸研究，（1997），25,109-111]，现在由密歇根州立大学微生物生态学中心主持。RDP-II是一个精心策划的数据库，提供核糖体RNA （rRNA）核苷酸序列数据，以对齐和未对齐的形式，分析服务和相关的计算机程序。在过去的两年中，数据比对已经更新，现在包括bbbb9700小亚基rRNA序列。最近开发的ObjectStore数据库将提供更快的数据更新、更好的数据准确性和更多的用户访问。RDP-II包括rma序列的系统发育有序比对，衍生的系统发育树，rRNA二级结构图，以及用于处理，分析和显示比对和树的各种软件程序。这些数据可以通过匿名ftp （ftp.cme.msu.edu）和WWW （http://www.cme.msu.edu/RDP）获得。WWW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、筛选可能的嵌合rRNA序列、自动比对以及在现有系统发育树上对未知序列的建议放置。RDP-II中还存在其他实用程序，包括距离矩阵、T-RFLP，以及可用于创建子树的基于java的系统发育树查看器。
The Ribosomal Database Project (RDP-II), previously described by Maidak ef 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 rRMA 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.