Abstract
Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.
Highlights
Ribosomal Database Project (RDP) 11.1, released in October 2013, contains 2 809 406 aligned and annotated bacterial and archaeal small subunit (SSU) rRNA gene sequences and 62 860 fungal large subunit (LSU) rRNA gene sequences
A relatively small percentage of bacterial and archaeal sequences originate from organisms in culture; roughly 85% and 97%, respectively, of bacterial and archaeal sequences in RDP are from DNA directly isolated from environmental samples
Over the past several years we have been approached by a number of researchers interested in using RDP tools for analysis of fungi in the environment. We are providing both an alignment of fungal 28S rRNA gene sequences and a fungal training set for the RDP Classifier leveraging a recently published phylogenetically consistent taxonomic mapping [4]
Summary
Ribosomal Database Project (RDP) 11.1, released in October 2013 (http://rdp.cme.msu.edu/), contains 2 809 406 aligned and annotated bacterial and archaeal small subunit (SSU) rRNA gene sequences and 62 860 fungal large subunit (LSU) rRNA gene sequences. We are providing both an alignment of fungal 28S rRNA gene sequences and a fungal training set for the RDP Classifier leveraging a recently published phylogenetically consistent taxonomic mapping [4].
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