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Antibiotic Dereplication Using the Antibiotic Resistance Platform
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Rfam: Wikipedia, clans and the "decimal" release.

Paul P Gardner1, Jennifer Daub, John Tate

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA. pg5@sanger.ac.uk

Nucleic Acids Research
|November 11, 2010
PubMed
Summary

The Rfam database catalogs non-coding RNAs using sequence alignments and covariance models. This study evaluates using Wikipedia for community annotation and discusses new features like RNA family clans.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • The Rfam database is a comprehensive catalog of non-coding RNAs.
  • It utilizes sequence alignments and covariance models for RNA family classification.
  • Accurate annotation is crucial for understanding RNA function and evolution.

Purpose of the Study:

  • To evaluate the utility of Wikipedia as a source for community-derived annotation in Rfam.
  • To report on recent developments within the Rfam database, including the introduction of clans.
  • To provide an updated overview of the Rfam resource and its accessibility.

Main Methods:

  • Analysis of the advantages and disadvantages of using Wikipedia for Rfam annotation.
  • Description of the methodology for grouping related RNA families into clans.
  • Overview of new features and improvements implemented on the Rfam website.

Main Results:

  • The study discusses the potential benefits and drawbacks of integrating community-generated data from Wikipedia.
  • New organizational structures, such as clans, have been implemented to better represent relationships between RNA families.
  • The Rfam website has undergone development to enhance user experience and data accessibility.

Conclusions:

  • Wikipedia offers a potential avenue for community-driven annotation, though challenges exist.
  • The integration of clans provides a more structured view of RNA family relationships.
  • Ongoing developments aim to improve the Rfam database as a valuable resource for non-coding RNA research.