Custom miRNA - target gene prediction by miRNA sequence

Question

[Adam]

Hello,

based on your experience, do you know any tool which allows to predict target gene for specific miRNA, however I mean novel miRNAs (for example result from miRDeep2) where I have only a sequence, read count, info about score and quality

At the moment I know two tools for analysis such like these:

miRDB: http://www.mirdb.org/custom.html

Old custom TargetScan(2011): http://www.targetscan.org//vert_50/seedmatch.html

Will you recommend tools above? Are there accurate? Do you know any packages for R to find previously mentioned predictions?

Thank you in advace.

[Buffo]

I think this would help you miRanda algorithm. It works for me.