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  • Palgrave
    Member
    • Aug 2011
    • 73

    match miRBase miRNAs to Targetscan

    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
    Senior Member
    • Mar 2010
    • 329

    #2
    Yes. Patman is a very simple tool for this task. More sophisticated one is miRanda.

    Comment

    • bharat_iyengar
      Member
      • Dec 2012
      • 20

      #3
      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.

      Comment

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