I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks in the distributions of my age. One idea I had was to check to see if these peaks correspond to periods of intense specialization. For instance, the Eutheria clade saw a vast diversification of species relative to other clades. I'd like to determine this from a more computational perspective rather than Googling each clade.

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    $\begingroup$ Can you clarify what exactly your question is? You want to phylogenetically classify using microRNAs?? $\endgroup$ – WYSIWYG Jul 26 '14 at 5:15

My guess (as your question need heavy editing!!) would be MiRdup.

MiRdup Goals:

  • Validation of pre-miRNAs predictions

  • Prediction of mature miRNA

Abstract: MicroRNAs (miRNAs) are short RNA species derived from hairpin-forming miRNA precursors (pre-miRNA) and acting as key post-transcriptional regulators. Most computational tools labeled as miRNA predictors are in fact pre-miRNA predictors and provide no information about the putative miRNA location within the pre-miRNA. Sequence and structural features that determine the location of the miRNA, and the extent to which these properties vary from species to species, are poorly understood. We have developed miRdup, a computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA. MiRdup is based on a random forest classifier trained with experimentally validated miRNAs from miRbase, with features that characterize the miRNA-miRNA* duplex

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