RRM
2010 Rustbelt RNA Meeting
RRM
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Poster abstracts
Abstract:
The Ribosomal Databse Project: Tools and sequences for rRNA analysis.
Benli Chai, Jordan A. Fish, Qiong Wang, James M. Tiedje and James R. Cole.
Center for Microbial Ecology, Michigan State University, 2225A Biomedical Physical Sciences, East Lansing, MI
The ribosomal small subunit rRNA (16S) gene is the most frequently used molecular marker
for studying microorganisms. The Ribosomal Database Project (RDP; http://rdp.cme.msu.edu) offers aligned and annotated 16S rRNA sequence data and analysis services to the research community. Updated monthly, RDP maintained 1,418,497 aligned and annotated quality-controlled public rRNA sequences as of September 2010, while researchers maintain over 5 million sequences in their myRDP accounts. RDP products are widely used in molecular phylogeny and evolutionary biology, microbial ecology, bacterial identification, characterizing microbial populations, and in understanding the diversity of life.
While Current-Generation sequencing technologies such as 454 and Illumina are transforming studies of microbial diversity by offering greatly extended sequencing breadth and depth, they also bring in challenges in data processing and analysis. The RDP Pyrosequencing Pipeline provides an effective toolkit to automate the computationally-intensive processing and analysis of these large datasets. The Pipeline takes raw high-throughput reads through initial processing steps to hierarchical clustering into OTUs or taxonomic assignment using the RDP Classifier. Several common ecological metrics are calculated including Chao1, Shannon Index and rarefaction. Results are available in formats suitable for common statistical and ecological packages. Other RDP tools include the RDP Classifier, also available as an open-source package; Sequence Match for finding nearest neighbors; Library Compare for determining differentially represented taxa between two libraries; RDP Probe Match for determining taxonomic coverage of primers and probes; Tree Builder for rapid phylogenetic tree construction; and Browsers that provide entry to the public sequences.
Keywords: rRNA, pyrosequencing, bioinformatics
