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

被引：3852

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

页码：D141 / D145

页数：5

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