The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

被引：3809
作者：
Cole, J. R. [1 ]
Wang, Q. [1 ]
Cardenas, E. [1 ]
Fish, J. [2 ]
Chai, B. [1 ]
Farris, R. J. [1 ]
Kulam-Syed-Mohideen, A. S. [1 ]
McGarrell, D. M. [1 ]
Marsh, T. [1 ,2 ]
Garrity, G. M. [2 ]
Tiedje, J. M. [1 ,2 ]
机构：
[1] Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA
[2] Michigan State Univ, Dept Microbiol & Mol Genet, E Lansing, MI 48824 USA
来源：
NUCLEIC ACIDS RESEARCH | 2009年 / 37卷
基金：
美国国家科学基金会;
关键词：
SEQUENCES; DIVERSITY; PHYLUM;
D O I：
10.1093/nar/gkn879
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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/.
引用
收藏
页码：D141 / D145
页数：5
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