The Ribosomal Database Project: Improved Alignments and New Tools for rRNA Analysis

Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.

Abstract

The Ribosomal Database Project (RDP) provides researchers with 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. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Graphics
  • Databases, Nucleic Acid*
  • Internet
  • RNA, Archaeal / chemistry*
  • RNA, Archaeal / classification
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / classification
  • RNA, Ribosomal / chemistry*
  • RNA, Ribosomal / classification
  • Sequence Alignment
  • Sequence Analysis, RNA*
  • Software

Substances

  • RNA, Archaeal
  • RNA, Bacterial
  • RNA, Ribosomal