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FAQ / Notes

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The PITA executable allows you to identify and score microRNA targets on UTRs. It is provided as an executable wrapped in Perl scripts, as described below.

NOTE:THIS SOFTWARE IS FREELY AVAILABLE FOR ACADEMIC USE ONLY, and is distributed under the The GNU Lesser General Public License.


  1. The executable is compiled for a 32 bit and for a 64 bit Linux machines. It is wrapped by Perl scripts.
  2. The executable uses the Vienna RNA package, which is developed by Ivo Hofacker at the Institute for Theoretical Chemistry of the University of Vienna.
    Latest version, Copyright information

Versions History

Last version is available here for download.
  • PITA executable version 1 (23-Sept-07): Initial release (not functional due to hardcoded paths).
  • PITA executable version 2 (30-Sept-07): Fixed hardcoded paths in one script and energy value signs (energies are now negative as should be).
  • PITA executable version 3 (17-Oct-07): Modified tab file output format
  • PITA executable version 4 (19-Jun-08): Minor bug fixes.
  • PITA executable version 5 (05-Aug-08): Outputs targets file in addition to sites file.
  • PITA executable version 6 (31-Aug-08): Seeds are preferably reported as short but fully-complement (an 8-mer with a G:U wobble at the last seed position will be reported as a 7-mer with no G:U wobbles); minor bug fixes.

Download Instructions

  1. Download the archive file into a folder of your choice. You can select between a 32-bit version: or a 64-bit one: (download the 32-bit version if unsure).
  2. Unzip and extract all its files (tar xvfz pita_prediction.tar.gz).
  3. Type make install


The main script is, type: --help to see its usage.

The main parameters the script expects are:
  • UTRs file - a fasta format file containing the UTR(s) to predict miRs on.
  • miRs file - a fasta format file containing the miR(s) sequences to use (known miRs for human, mouse, fly and worm are contained in the zip file, under the known_mirs directory).

The download zip file contains example files:
  • input_utr.fa - example UTR file
  • input_microRNAs.fa - example microRNAs file
  • - tab delimited table of predictions results
  • - tab delimited table of targets
  • example_pita_results.gxp - gxp file (Genomica project file) with chromosome tracks of the UTR(s) and the miRs predictions.
These output files were produced by this command:
./ -utr input_utr.fa -mir input_microRNAs.fa -prefix example -gxp

For troubleshooting and FAQ please visit our executables FAQ page.