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MicroRNAs (miRNAs) are small, single stranded RNAs with a key role in post-transcriptional regulation of thousands of genes across numerous species. While several computational methods are currently available for identifying miRNA genes, accurate prediction of the mature miRNA remains a challenge. Existing approaches fall short in predicting the location of mature miRNAs but also in finding the functional strand(s) of miRNA precursors. MatureBayes is a computational tool that incorporates a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. We take into account both positive (true mature miRNAs) and negative (same-size non-mature miRNA sequences) examples to optimize sensitivity as well as specificity. Our method can accurately predict the start position of experimentally verified mature miRNAs for both human and mouse, achieving a significantly larger (often double) performance accuracy compared with two existing methods. Moreover, the method exhibits a very high generalization performance on miRNAs from two other organisms. More importantly, our method provides direct evidence about the features of miRNA precursors which may determine the location of the mature miRNA. We find that the triplet of positions 7, 8 and 9 from the mature miRNA end towards the closest hairpin have the largest discriminatory power, are relatively conserved in terms of sequence composition (mostly contain a Uracil) and are located within or in very close proximity to the hairpin loop, suggesting the existence of a possible recognition site for Dicer and associated proteins


  • MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors.
    Gkirtzou Katerina, Tsamardinos Ioannis, Tsakalides Panagiotis and Poirazi Panagiota.
    PLoS One, 2010
    [pdf] [bibtex]
  • Mature miRNA identification via the use of a Naive Bayes Classifier
    Gkirtzou Katerina
    Master of Science, University of Crete, 2009
    [pdf] [bibtex] [presentation]
  • Mature miRNA Identification via the Use of a Naive Bayes Classifier.
    Gkirtzou Katerina, Tsakalides Panagiotis and Poirazi Panagiota.
    8th IEEE International Conference on BioInformatics and BioEngineering (BIBE), 2008
    [pdf] [bibtex]


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