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Bioinformatics. 2004 Nov 22;20(17):2911-7. Epub 2004 Jun 24.

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.

Author information

1
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.

Abstract

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.

PMID:
15217813
DOI:
10.1093/bioinformatics/bth374
[Indexed for MEDLINE]
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