A comparison of RNA folding measures View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2005-12

AUTHORS

Eva Freyhult, Paul P Gardner, Vincent Moulton

ABSTRACT

BACKGROUND: In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. RESULTS: Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. CONCLUSION: Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score) and the other to see if the sequence has a unique fold (the average base-pair distance, D). More... »

PAGES

241

References to SciGraph publications

  • 1999-07. Estimating the Contributions of Selection and Self-Organization in RNA Secondary Structure in JOURNAL OF MOLECULAR EVOLUTION
  • 1994-02. Fast folding and comparison of RNA secondary structures in MONATSHEFTE FÜR CHEMIE - CHEMICAL MONTHLY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2105-6-241

    DOI

    http://dx.doi.org/10.1186/1471-2105-6-241

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16202126


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