mirLSTM: A Deep Sequential Approach to MicroRNA Target Binding Site Prediction

Abstract

MicroRNAs (miRNAs) are small and non-coding RNAs of similar to 21-23 base length, which play critical role in gene expression. They bind the target mRNAs in the post-transcriptional level and cause translational inhibition or mRNA cleavage. Quick and effective detection of the binding sites of miRNAs is a major problem in bioinformatics. In this study, a deep learning approach based on Long Short Term Memory (LSTM) is developed with the help of an existing duplex sequence model. Compared with four conventional machine learning methods, the proposed LSTM model performs better in terms of the accuracy (ACC), sensitivity, specificity, AUC (Area under the curve) and F1 score. A web-tool is also developed to identify and display the microRNA target sites effectively and quickly.