核糖体数据库项目II(RDP-II)

The RDP-II (Ribosomal Database Project).

作者信息

Maidak B L, Cole J R, Lilburn T G, Parker C T, Saxman P R, Farris R J, Garrity G M, Olsen G J, Schmidt T M, Tiedje J M

机构信息

Center for Microbial Ecology, 540 Plant and Soil Sciences Building, Michigan State University, East Lansing, MI 48824-1325, USA.

出版信息

Nucleic Acids Res. 2001 Jan 1;29(1):173-4. doi: 10.1093/nar/29.1.173.

Abstract

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.

摘要

核糖体数据库项目(RDP-II),先前由迈达克等人描述[《核酸研究》(2000年),28卷,173 - 174页],在过去一年继续向比对数据中添加新的rRNA序列并改进分析命令。8.0版本(2000年6月1日)包含16277条比对后的原核生物小亚基(SSU)rRNA序列,而比对形式的真核生物和线粒体SSU rRNA序列数量分别保持在2055条和1503条。原核生物SSU rRNA序列数量比14个月前的上一版本增加了一倍多,约75%的序列长度超过899 bp。日本现在有一个RDP-II镜像站点(http://wdcm.nig.ac.jp/RDP/html/index.html)。RDP-II通过其万维网服务器(http://rdp.cme.msu.edu/)提供比对和注释的rRNA序列、推导的系统发育树和分类层次结构以及分析服务。分析服务包括rRNA探针检查、用户序列的近似系统发育定位、筛选用户序列中可能的嵌合rRNA序列、自动比对、生成相似性矩阵以及规划和分析末端限制性片段多态性实验的服务。用于提问和评论的RDP-II电子邮件地址已从curator@cme.msu.edu更改为rdpstaff@msu.edu。

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