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Nucleic Acids Research Advance Access published online on November 12, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn879
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

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

J. R. Cole1,*, Q. Wang1, E. Cardenas1, J. Fish2, B. Chai1, R. J. Farris1, A. S. Kulam-Syed-Mohideen1, D. M. McGarrell1, T. Marsh1,2, G. M. Garrity2 and J. M. Tiedje1,2

1Center for Microbial Ecology and 2Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA

*To whom correspondence should be addressed. Tel: +1 517 353 3842; Fax: +1 517 353 8957; Email: colej{at}msu.edu

Received September 15, 2008. Revised October 16, 2008. Accepted October 17, 2008.

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/.


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