Ribosomal Database Project: data and tools for high throughput rRNA analysis

The bacterial and archaeal aligners were trained using secondary structure information from the Comparative RNA Web Site and training alignments we developed with 2591 bacterial and 144 archaeal full-length sequences mostly from sequenced genomes, respectively

James R. Cole; Qiong Wang; Jordan A. Fish; Benli Chai; Donna M. McGarrell; Yanni Sun; C. Titus Brown; Andrea Porras-Alfaro; Cheryl R. Kuske; James M. Tiedje

2013

Scholarcy highlights

  • Ribosomal Database Project 11.1, released in October 2013, contains 2 809 406 aligned and annotated bacterial and archaeal small subunit rRNA gene sequences and 62 860 fungal large subunit 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
  • The bacterial and archaeal aligners were trained using secondary structure information from the Comparative RNA Web Site and training alignments we developed with 2591 bacterial and 144 archaeal full-length sequences mostly from sequenced genomes, respectively
  • For researchers processing a moderate amount of sequences, we offer online versions of the RDPipeline tools
  • For researchers involved in high-volume sequencing projects, or who would like to incorporate some of our tools into their local custom workflow, we offer all the tools that make up the RDPipeline on the RDP GitHub repository
  • The ‘Sequence Selector’ tool allows researchers to upload a set of sequence files and a separate file containing a list of IDs. A file is returned either containing only the sequences specified, or excluding them, depending on option selected

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