RNA-RNA interactions play a major role in gene expression. Most of the present methods of RNA-RNA interactions are based on minimum free energy and alignments. Methods that are based on minimum free energy give good results but the alignment based methods are also used in their conjunction.
Recently Umu et. al. (2017) have taken into account all the different interaction predicting algorithms to develop a script which accurately determines all the RNA-RNA interactions. The script can be accessed at the following URL:(github.com/UCanCompBio/RNA_Interactions_Benchmark)
Umu S.U. et.al. (2017) A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics 33 (7):988-996