sRNARFTarget – a fast machine-learning-based approach for transcriptome-wide sRNA target prediction

Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A key step to understand sRNAs function is to identify the mRNAs these sRNAs bind to. There are several computational methods for sRNA target prediction, and the most accurate one is CopraRNA which is based on comparative-genomics. However, species-specific sRNAs are quite common and CopraRNA cannot be used for these sRNAs. The most commonly used transcriptome-wide sRNA target prediction method and second-most-accurate method is IntaRNA. However, IntaRNA can take hours to run on a bacterial transcriptome.

Researchers at Memorial University of Newfoundland have developed sRNARFTarget, a machine-learning-based method for transcriptome-wide sRNA target prediction applicable to any sRNA. The researchers comparatively assessed the performance of sRNARFTarget, CopraRNA and IntaRNA in three bacterial species. Their results show that sRNARFTarget outperforms IntaRNA in terms of accuracy, ranking of true interacting pairs, and running time. However, CopraRNA substantially outperforms the other two programs in terms of accuracy. Thus, the researchers suggest using CopraRNA when homolog sequences of the sRNA are available, and sRNARFTarget for transcriptome-wide prediction or for species-specific sRNAs.

Workflow of sRNARFTarget prediction-interpretation programs

Availability – sRNARFTarget is available at https://github.com/BioinformaticsLabAtMUN/sRNARFTarget.