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FAQ / Notes

Online microRNA prediction tool


This tool allows you to run the PITA algorithm on your choice of UTRs and microRNAs. PITA starts by scanning the UTR for potential microRNA targets (using the supplied seed matching tools) and then scores each site using the method described in Kertesz et al., The role of site accessibility in microRNA target recognition, Nature Genetics 2007.

The tool is limited to 100 targets per run. For heavy-duty microRNA prediction, please download the PITA executable and run it on your own machine.


Select an organism:

Paste UTR sequence (fasta format) Or upload: Paste input example

 Use all known human microRNAs (470).
 Upload microRNAs to use





Advanced Parameters


 Use filler upstream sequence
 Specify upstream sequence (optional, improves results accuracy)

Minimum seed size
Allow single G:U
Allow single mismatch
Flank settings
For more flexible seed-matching criteria (e.g. allow two G:U wobbles or loops) and flank settings please download and run the PITA executable.


For problems and questions, please e-mail Eran Segal