piRNA is a parallel C++ package to compute joint and individual partition functions for two RNA sequences. From the partition functions, piRNA computes equilibrium concentrations of single and double joint species, ensemble energy, and melting temperatures.

Web Server

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Binary for Linux

piRNA version 3.3 binary for linux (compiled with gcc x86_64 4.3.2)


Run 'partition' with '-h' or '--help' option.



A collection of '.dG' files containing the partition function and ensemble energy.

Please cite

A Partition Function Algorithm for Interacting Nucleic Acid Strands --[Supplementary Materials]
Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
Bioinformatics 25(12), to appear
Also, 17th Annual International Conference on Intelligent Systems for Molecular Biology ISMB/ECCB 2009