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Related Experiment Videos

PseudoBase: a database with RNA pseudoknots.

F H van Batenburg1, A P Gultyaev, C W Pleij

  • 1Group Theoretical Biology, Institute of Evolutionary and Ecological Sciences, Leiden University, Kaiserstraat 63, 2311GP Leiden, The Netherlands. batenburg@rulsfb.leidenuniv.nl

Nucleic Acids Research
|December 11, 1999
PubMed
Summary
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PseudoBase is a new database for RNA pseudoknots, offering structural, functional, and sequence data. It allows users to retrieve existing data or submit new RNA pseudoknot information.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA pseudoknots are complex secondary structures crucial for RNA function.
  • Existing databases may lack comprehensive data on RNA pseudoknots.
  • Efficient data management and retrieval are essential for RNA research.

Purpose of the Study:

  • To introduce PseudoBase, a comprehensive database for RNA pseudoknots.
  • To provide a centralized resource for structural, functional, and sequence data of RNA pseudoknots.
  • To facilitate the submission and retrieval of RNA pseudoknot information.

Main Methods:

  • Development of a relational database to store pseudoknot data.
  • Implementation of a user-friendly web interface for data access and submission.

Related Experiment Videos

  • Utilizing an evolutionary methodology for database development.

    • Main Results:

    • PseudoBase stores 12 key data items per pseudoknot, including sequence, structure, and reliability information.
    • The database provides access to EMBL accession numbers for sequences containing pseudoknots.
    • A structured access system with 16 categories simplifies data retrieval.

    Conclusions:

    • PseudoBase serves as a valuable resource for researchers studying RNA pseudoknots.
    • The database enhances accessibility to critical RNA pseudoknot data.
    • The evolutionary development approach ensured a robust and adaptable database structure.