The Ribosomal Database Project: improved alignments and new tools for rRNA analysis - PubMed (original) (raw)

. 2009 Jan;37(Database issue):D141-5.

doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.

Affiliations

• PMID: 19004872
• PMCID: PMC2686447
• DOI: 10.1093/nar/gkn879

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.

Tools available in the RDP for processing pyrosequencing data.

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).

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