match miRBase miRNAs to Targetscan

[Palgrave]

Dear everyone,
I was looking for a way to get targets for the miRBase miRNAs out of TargetScan. TargetScan mainly operates with families and often don't have information about 3p/5p for the different miRNAs. Is there a way to match the miRNA fasta sequence from miRBase to get TargetScan targets?

[TiborNagy]

Yes. Patman is a very simple tool for this task. More sophisticated one is miRanda.

[bharat_iyengar]

Even with targetscan you can build your own families.. It is pretty cumbersome. It is not straightforward. With miRanda you can do a fasta vs fasta prediction and it is fairly simple. You can add more parameters to control the stringency. Unfortunately the TargetScan database is not updated and doesn't have 3p/5p information.