Sfold Tools for MicroRNA Target Prediction

Computational prediction of miRNA-binding sites on target mRNAs facilitates experimental investigation of miRNA functions. In this chapter, we describe the command-line use of STarMir, an application module of the Sfold RNA package. STarMir performs miRNA-binding site predictions for target RNAs. Output data include comprehensive sequence, thermodynamic, and target structure features, a logistic probability measuring confidence for each predicted site and a quantitative score. Based on a large 3' UTR assay dataset, this score provides a quantitative measure of the overall regulatory effects of both seed and seedless sites on the target. Sfold is now on Wikipedia at https://en.wikipedia.org/wiki/Sfold . STarMir and the rest of the Sfold package can be downloaded from GitHub at https://github.com/Ding-RNA-Lab/Sfold .