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Related Experiment Videos

Predicting RNA structure using mutual information.

Eva Freyhult1, Vincent Moulton, Paul Gardner

  • 1The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. eva.freyhult@lcb.uu.se

Applied Bioinformatics
|July 8, 2005
PubMed
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MIfold, a new MATLAB toolbox, uses mutual information to predict conserved RNA secondary structures, including pseudoknots, from alignments. It offers adjustable sensitivity and selectivity, aiding RNA database development.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Increasing numbers of sequenced RNAs and databases necessitate accurate, automated RNA structure prediction.
  • RNA secondary structures are evolutionarily conserved, making covariation analysis a valuable tool.
  • Existing tools may not fully leverage mutual information for comprehensive structure prediction.

Purpose of the Study:

  • To present MIfold, a MATLAB toolbox for predicting conserved RNA secondary structures, including pseudoknots, from multiple sequence alignments.
  • To demonstrate the utility of mutual information and related covariation measures in RNA structure prediction.
  • To evaluate MIfold's performance and compare it with existing software.

Main Methods:

  • Development of the MIfold MATLAB toolbox.

Related Experiment Videos

  • Application of mutual information and covariation measures to identify covarying sites in RNA alignments.
  • Prediction of RNA secondary structures, including pseudoknots.

    • Main Results:

    • MIfold successfully predicts simple pseudoknots with adjustable sensitivity and selectivity.
    • Performance of MIfold improves with an increased number of aligned sequences for certain RNA types.
    • MIfold shows higher sensitivity but lower selectivity than RNAalifold, and comparable performance to COVE.

    Conclusions:

    • MIfold serves as a valuable supplementary tool for RNA structure prediction.
    • It is useful for automatically generating structural predictions for RNA databases like Rfam.
    • MIfold enhances existing bioinformatics workflows for RNA structure analysis.