rpiCOOL: A tool for In Silico RNA–protein interaction detection using random forest

• New encoding schema for RNA sequence based on recently experimentally validated RNA-protein interactions. “repetitive sequence patterns" and “nucleotide composition” features contribute effectively in RPI detection.
• Using appropriate computational models that were trained using encoding schema based on the new findings of experimental studies could produce an accurate tool to RPI prediction.
• The challenge the RPI prediction could vary considerably across different organisms.
• The proposed method have been implemented as a stand-alone tool with a user friendly graphical user interface (GUI) that enables the researchers to predict RNA-protein interaction.

Understanding the principle of RNA–protein interactions (RPIs) is of critical importance to provide insights into post-transcriptional gene regulation and is useful to guide studies about many complex diseases. The limitations and difficulties associated with experimental determination of RPIs, call an urgent need to computational methods for RPI prediction. In this paper, we proposed a machine learning method to detect RNA–protein interactions based on sequence information. We used motif information and repetitive patterns, which have been extracted from experimentally validated RNA–protein interactions, in combination with sequence composition as descriptors to build a model to RPI prediction via a random forest classifier. About 20% of the “sequence motifs” and “nucleotide composition” features have been selected as the informative features with the feature selection methods. These results suggest that these two feature types contribute effectively in RPI detection. Results of 10-fold cross-validation experiments on three non-redundant benchmark datasets show a better performance of the proposed method in comparison with the current state-of-the-art methods in terms of various performance measures. In addition, the results revealed that the accuracy of the RPI prediction methods could vary considerably across different organisms. We have implemented the proposed method, namely rpiCOOL, as a stand-alone tool with a user friendly graphical user interface (GUI) that enables the researchers to predict RNA–protein interaction. The rpiCOOL is freely available at http://biocool.ir/rpicool.html for non-commercial uses.