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The RDP (Ribosomal Database Project)

B L Maidak1, G J Olsen, N Larsen

  • 1Department of Microbiology, University of Illinois, B103 C&LSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA. b-maidak@uiuc.edu

Nucleic Acids Research
|January 1, 1997
PubMed
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The Ribosomal Database Project (RDP) provides curated ribosome data and analysis tools. It offers phylogenetic alignments, trees, and software for ribosomal RNA (rRNA) sequence analysis, aiding in phylogenetic placement and quality control.

Area of Science:

  • Microbiology
  • Bioinformatics
  • Molecular Biology

Background:

  • The Ribosomal Database Project (RDP) is a vital resource for researchers studying ribosomal RNA (rRNA).
  • It provides comprehensive data and computational tools essential for analyzing rRNA sequences and their evolutionary relationships.

Purpose of the Study:

  • To present the Ribosomal Database Project (RDP) as a curated resource for ribosome-related data.
  • To detail the analysis services, software, and data accessibility offered by the RDP.
  • To highlight the utility of RDP's tools for phylogenetic analysis and sequence quality assessment.

Main Methods:

  • Curated collection and organization of ribosomal RNA (rRNA) sequence data.
  • Development of phylogenetically ordered alignments and phylogenetic trees.

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  • Creation of software for sequence handling, analysis, and visualization.
  • Implementation of web-based and electronic mail servers for data access and analysis services.

    • Main Results:

    • RDP offers phylogenetically ordered alignments of rRNA sequences and derived phylogenetic trees.
    • Users can access data via anonymous FTP, electronic mail, gopher, and the World Wide Web (WWW).
    • Web and email servers provide services including probe checking, phylogenetic placement, chimeric sequence screening, and automated alignment.

    Conclusions:

    • The Ribosomal Database Project (RDP) serves as a comprehensive, user-friendly resource for ribosome research.
    • Its integrated data and analysis services facilitate advanced phylogenetic studies and quality control of rRNA sequences.
    • RDP enhances the accessibility and utility of ribosome-related information for the scientific community.