2008 | J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity and J. M. Tiedje
The Ribosomal Database Project (RDP) provides 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. New features include a Pyrosequencing Pipeline for analyzing ultra high-throughput rRNA sequencing data, a Taxomatic visualization tool for identifying taxonomic inconsistencies, and a class Assignment Generator for educational purposes. The RDP maintains 33,082 archaeal and 643,916 bacterial small subunit rRNA sequences, with 5534 sequences from species type-strains. The RDP sequence collection is updated monthly from INSDC. The RDP 10 release introduced new alignments based on Infernal, which is faster and more accurate than RNAcad. The RDP also provides a new phylogenetically consistent bacterial taxonomy and a Genome Browser feature. The RDP Pyrosequencing Pipeline automates data processing and simplifies analysis of large sequencing libraries. The Taxomatic visualization tool displays a color heatmap for identifying taxonomic inconsistencies. The RDP Classifier is a standalone program for classifying rRNA sequences. The RDP also offers educational tools for teaching rRNA analysis. The RDP provides user surveys and video tutorials for assistance. The RDP data and services are available at http://rdp.cme.msu.edu/. The RDP is supported by various funding sources and has no conflict of interest.The Ribosomal Database Project (RDP) provides 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. New features include a Pyrosequencing Pipeline for analyzing ultra high-throughput rRNA sequencing data, a Taxomatic visualization tool for identifying taxonomic inconsistencies, and a class Assignment Generator for educational purposes. The RDP maintains 33,082 archaeal and 643,916 bacterial small subunit rRNA sequences, with 5534 sequences from species type-strains. The RDP sequence collection is updated monthly from INSDC. The RDP 10 release introduced new alignments based on Infernal, which is faster and more accurate than RNAcad. The RDP also provides a new phylogenetically consistent bacterial taxonomy and a Genome Browser feature. The RDP Pyrosequencing Pipeline automates data processing and simplifies analysis of large sequencing libraries. The Taxomatic visualization tool displays a color heatmap for identifying taxonomic inconsistencies. The RDP Classifier is a standalone program for classifying rRNA sequences. The RDP also offers educational tools for teaching rRNA analysis. The RDP provides user surveys and video tutorials for assistance. The RDP data and services are available at http://rdp.cme.msu.edu/. The RDP is supported by various funding sources and has no conflict of interest.