Ribosomal database project

To date, the Ribosomal Database Project (RDP) release contains over 2.7 million sequences and counting (9) (Figure 1). 

BL Maidak, N Larson, MJ McCaughey, R Overbeek, GJ Olsen, K Eogel, J Blandy, CR Woese. The ribosomal database project. Nucleic Acids Res 22 3485-3487, 1994. 

One prerequisite for the molecular assessment of microbial diversity in natural environments is the availability of an extensive molecular database of cultured organisms which serve as a reference for the comparison of sequences from both isolates and uncultured strains. The comparison of sequences fi om environmental rDNA clone sequences to each other and to cultured strains will not only allow determination of the phylogenetic distance between the gene sequences but they will also facilitate the recognition of putative target sites for oligonucleotides, suitable for the specific detection of the respective strains directly in their natural habitat. The 16S rDNA database is already so extensive that about 90% of all described species can be placed rather accurately within the radiation of the main lines of descent. Examples for large 16S rDNA databases are the Ribosomal Database Project [9] and ARB [10]. 

Cole JR, Wang Q, Cardenas E, et al. The ribosomal database project improved alignments and new tools for rRNA analysis. Nucl Acids Res. 2009 37 D141 5. doi 10.1093/nar/gkp353. 

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014 42(D1) D633-D642. 

Cole, J.R., Chai, B., Farris, R.J., Wang, Q. et al.. The Ribosomal Database Project (RDP-II) sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33, D294—D296 (2005). 

Fig. 5 Taxonomic profiles frran the superkingdom bacteria of different biogas mitaobial communities based on analysis of metagenome sequcmce reads created by next-generation sequencing techniques. Phylogenetic class is indicated. The authms ctnnpared eithCT 16S-rDNA sequences or environmental gene tags (EGTs) with different referoice data sets, e.g., Ribosomal Database Project Classifier or ARB Database (modified aftta- Wirth et al. 2012 Krbber et al. 2009 Krause et al. 2008)...

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