Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA, Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA, Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Biological Sciences, Western Illinois University, Malcomb, IL 61455, USA and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244. Epub 2013 Nov 27.
Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.
核糖体数据库项目（RDP；http://rdp.cme.msu.edu/）为研究人员提供了已比对和注释的 rRNA 基因序列数据，以及可用于在 RDP 框架中分析自身 rRNA 基因序列的工具。RDP 数据和工具被广泛应用于人类健康、微生物生态学、环境微生物学、核酸化学、分类学和系统发生学等领域。除了已比对和注释的细菌和古菌小亚基 rRNA 基因集合外，RDP 现在还包括一个真菌大亚基 rRNA 基因集合。RDP 工具，包括 Classifier 和 Aligner，已更新以支持这个新的真菌集合。利用高通量测序来描述环境微生物种群在过去几年中迅速发展，并且随着测序技术的改进，环境数据集的规模也在不断增加。随着版本 11 的发布，RDP 提供了一组扩展的工具，以方便对高通量数据进行分析，包括单链和配对末端读取。此外，现在大多数工具都可以作为开源软件包下载，供有大容量需求的研究人员或希望开发自定义分析管道的人员在本地使用。
