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RALEE--RNA ALignment editor in Emacs.

Sam Griffiths-Jones1

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

Bioinformatics (Oxford, England)
|September 21, 2004
PubMed
Summary

RNA sequence alignment requires manual editing and structure prediction. The RNA Alignment Editor in Emacs (RALEE) tool simplifies this process by integrating structure-specific features into a widely used text editor.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • High-quality multiple sequence alignments of structured RNAs are crucial for biological research.
  • Existing RNA alignment editors often lack features for integrating secondary structure predictions.
  • Manual editing and computational structure prediction are typically used iteratively.

Purpose of the Study:

  • To introduce the RNA Alignment Editor in Emacs (RALEE) tool.
  • To provide a user-friendly environment for RNA multiple sequence alignment editing.
  • To enhance RNA alignment editing by incorporating structure-specific functionalities.

Main Methods:

  • RALEE is developed as an extension of the Emacs text editor.
  • It incorporates structure-specific color schemes to visualize alignment quality.
  • The tool utilizes external applications for RNA secondary structure prediction.

Main Results:

  • RALEE offers a simplified yet powerful environment for RNA alignment editing.
  • It effectively integrates secondary structure information into the alignment process.
  • The editor supports conventional text editing functions alongside specialized RNA features.

Conclusions:

  • RALEE addresses the need for alignment editors that support structure-based RNA analysis.
  • The tool's integration with Emacs ensures broad accessibility across various operating systems.
  • RALEE facilitates more accurate and efficient RNA multiple sequence alignment.

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