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Bioinformatic tools for novel miRNA target prediction - (Sep/10/2011 )

I am looking for some means to have a hint about the targets of some unknown micro RNAs. Are there any bioinformatic tools that can predict the target of an unknown micro RNA? The micro RNA sequences in my hand are not related to known classes of miRNAs. My experimental organism is Drosophila. Any suggestions will be greatly appreciated


miRanda or targetscan


You can use miRanda to predict targets for a unknown miRNA. It allows you to have two input files one containing miR sequences and the other mRNA sequences. miRanda can be downloaded here