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RNAlien - Unsupervised RNA family model construction.

Florian Eggenhofer1, Ivo L Hofacker2, Christian Höner Zu Siederdissen3

  • 1Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science University of Freiburg, Georges-Köhler-Allee, 79110 Freiburg, Germany egg@informatik.uni-freiburg.de.

Nucleic Acids Research
|June 23, 2016
PubMed
Summary
This summary is machine-generated.

RNAlien automates the discovery of RNA families from single sequences. This computational method builds RNA family models, reducing the need for extensive wet-lab experiments and expert manual curation.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Determining non-coding RNA function is challenging due to costly wet-lab experiments.
  • Computational methods, like homology searches, are crucial for annotating newly sequenced genomes.
  • Existing covariance models require known family examples and expert manual alignment/structure curation.

Purpose of the Study:

  • To develop an automated computational method for RNA family identification and model construction.
  • To reduce reliance on manual curation and extensive experimental validation for RNA functional annotation.

Main Methods:

  • RNAlien utilizes iterative homology searches starting from a single RNA sequence.
  • The method automatically constructs RNA family covariance models based on identified homologous sequences.
  • Validation was performed using a subset of the Rfam RNA family database.

Main Results:

  • RNAlien successfully constructs RNA family models automatically.
  • The generated models serve as a foundation for creating sensitive and specific RNA family classifications.
  • Performance is comparable to manually curated models from the Rfam database.

Conclusions:

  • RNAlien offers an efficient, automated approach to RNA family annotation.
  • The tool significantly lowers the barrier for discovering RNA function and family membership.
  • RNAlien is available as a tool and web server for broader scientific use.