Cole J R, Wang Q, Cardenas E, Fish J, Chai B, Farris R J, Kulam-Syed-Mohideen A S, McGarrell D M, Marsh T, Garrity G M, Tiedje J M
Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.
The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.
核糖体数据库项目（RDP）为研究人员提供了经过质量控制的细菌和古菌小亚基rRNA比对及分析工具。一种改进的比对策略使用了Infernal二级结构感知比对器，以提供更一致的高质量比对，并更快地处理用户序列。大量新的分析功能包括一个新的焦磷酸测序管道，它提供了支持超高通量rRNA测序数据分析的工具。这个管道提供了一组工具，可自动进行数据处理并简化对大型测序文库的计算密集型分析。此外，一个新的Taxomatic可视化工具可快速可视化分类不一致情况并给出修正建议，还有一个新的类别分配生成器为教师提供教案和个性化教材。有关RDP数据和分析功能的详细信息可在http://rdp.cme.msu.edu/上找到。
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