The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
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
[Article] Nucleic Acids Research. 37 Database issue:D141-D145, January 2009.

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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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