Bioinformatics Advance Access originally published online on June 24, 2004
Bioinformatics 2004 20(17):2911-2917; doi:10.1093/bioinformatics/bth374
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.
Discovery Note |
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
1 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium and 2 Laboratoire associé de l'INRA, France
Received on January 21, 2004; revised on June 2, 2004; accepted on June 17, 2004
Advance Access Publication June 23, 2004
Motivation: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the folding energy of the secondary structure of non-coding RNA sequences, such as microRNA precursors, transfer RNAs and ribosomal RNAs in several eukaryotic taxa. Statistical biases are assessed by a randomization test, in which the predicted minimum free energy of folding is compared with values obtained for structures inferred from randomly shuffling the original sequences.
Results: In contrast with transfer RNAs and ribosomal RNAs, the majority of the microRNA sequences clearly exhibit a folding free energy that is considerably lower than that for shuffled sequences, indicating a high tendency in the sequence towards a stable secondary structure. A possible usage of this statistical test in the framework of the detection of genuine miRNA sequences is discussed.
Availability: The dataset, software and additional data files are freely available as supplementary information on our Website.
Supplementary information: http://www.psb.ugent.be/bioinformatics/
Contact: yves.vandepeer{at}psb.ugent.be
* To whom correspondence should be addressed.
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