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prediction of microRNA targets using the sequence - (Jul/16/2014 )

Hi everyone!

I am working with small RNA sequencing and I am interested in predicting the putative targets of  microRNAs that are not annotated in mirBase (new microRNAs that we have identified with deep sequencing).

Do you know if there is any prediction tool (similar to targetscan, mirwalk, Pictar,..) that gives the list of potencial targets introducing just the sequence of the microRNA instead of the name of the microRNA?

Thank you for your help! 


You can use command line miRanda program to run target prediction.


1. download the program from this page (at the bottom)

2. format your miRNA or small RNA sequences in FASTA format (you can give any unique ID to each sequence. The format will look like this:






3. download sequences again which targets are to be predicted as fasta file. For example you can download all 3UTR sequences of an organism using BioMart tool

4. run the program in a linux environment, or a virtual linux environment in windows or mac.