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. 2009 Jan;37(Database issue):D141-5.
doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.

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

J R Cole  1 , Q Wang, E Cardenas, J Fish, B Chai, R J Farris, A S Kulam-Syed-Mohideen, D M McGarrell, T Marsh, G M Garrity, J M Tiedje
Affiliations

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

J R Cole et al. Nucleic Acids Res. 2009 Jan.

Abstract

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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Figures

Figure 1.
Figure 1.
Tools available in the RDP for processing pyrosequencing data.
Figure 2.
Figure 2.
Taxomatic sample screenshot demonstrating a taxonomic anomaly. Yellow indicates more close sequences and teal more distant, with intermediate distances black. The screen is zoomed-in to show a portion of proteobacterial type-strain sequences. α: Alphaproteobacteria. β: Betaproteobacteria. The mouse points to the genus Shinella, originally placed in the Alphaproteobacteria (21), but incorrectly moved to the Betaproteobacteria in the Taxonomic Outline of the Bacteria and Archaea (9).
See this image and copyright information in PMC

References

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