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Related Experiment Videos

Rfam: an RNA family database.

Sam Griffiths-Jones1, Alex Bateman, Mhairi Marshall

  • 1The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. sgj@sanger.ac.uk

Nucleic Acids Research
|January 10, 2003
PubMed
Summary

Rfam is a comprehensive database of non-coding RNA families, featuring multiple sequence alignments and covariance models. This resource aids in identifying and annotating RNA genes across various taxonomic divisions.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Non-coding RNAs (ncRNAs) play crucial roles in cellular processes.
  • Identifying and classifying ncRNA families is essential for understanding gene regulation.
  • Existing databases may lack comprehensive annotations or standardized models.

Purpose of the Study:

  • To introduce Rfam, a centralized database for non-coding RNA families.
  • To provide robust tools for searching and annotating ncRNA genes.
  • To facilitate the study of ncRNA evolution and function.

Main Methods:

  • Collection and curation of multiple sequence alignments for ncRNA families.
  • Development of covariance models for sensitive ncRNA detection.
  • Web-based interfaces for sequence searching and data visualization.

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  • Local database download and analysis using the INFERNAL package.

    • Main Results:

    • Rfam release 1.0 includes 25 curated ncRNA families.
    • The database annotates over 50,000 non-coding RNA genes.
    • Web and local search tools enable efficient identification of ncRNA genes.
    • Data is integrated with the EMBL nucleotide database.

    Conclusions:

    • Rfam provides a valuable, integrated resource for ncRNA research.
    • The database and associated tools enhance the discovery and annotation of ncRNAs.
    • Rfam supports comparative genomics and functional studies of non-coding RNAs.