The computational predicted binding interactions between human tRFs and target transcripts are based on the state-of-the-art prediction tools RNAhybrid and IntaRNA.
RNAhybrid is an old but still popular tool. It is a free energy-based tool, and utilizes the Dynamic Programming technique to efficiently calculate the optimal and more suboptimal interaction sites. The detailed setting of RNAhybrid are shown as below:
IntaRNA is also a free energy-based tool, and the only difference with RNAhybrid is IntaRNA incorporates the “accessibility” feature. The detailed setting of IntaRNA are shown as below: