There are numerous bioinformatics tools nowadays which predict the targets of a given miRNA. Is there any tool/ software to find the microRNAs regulating a mRNAs and is there a rule guiding microRNA prediction targets ?
I believe the miRSearch is the best. This article might be helpful.
http://www.exiqon.com/microrna-target-prediction
Give a try in already answered questions,
Here is my previous reply that will help you
Herein I list 4 tools most used small RNA-Seq:
1) Based on Encode
https://www.encodeproject.org/pipelines/ENCPL337CSA/
2) iSmaRT
http://bioinformatics.oxfordjournals.org/content/early/2017/01/05/bioinformatics.btw734.abstract
3) iMir
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-362
4) miRDeep2
https://www.mdc-berlin.de/8551903/en/
Hope this helps you!
Any recommendation for a bioinformatic pipeline for small RNA sequencing?. Available from: https://www.researchgate.net/post/any_recommendation_for_a_bioinformatic_pipeline_for_small_RNA_sequencing [accessed May 26, 2017].
After getting the output of predicted gene targets I would then recommend filtering your list based on whether the target is expressed in your cells/tissue of interest.
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