iEnhancer-RD: Identification of enhancers and their strength using RKPK features and deep neural networks

Enhancers are regulatory elements involved in gene expression.It is a part of DNA, which can enhance the transcription rate of gene. However, the identification of enhancer by biological experimental methods is time-consuming and expensive. Therefore, there is an urgent need for more efficient methods to identify them.In this study, we propose a new feature extraction method RKPK, which combines three feature methods and uses the recursive feature elimination algorithm for feature selection, and apply deep neural network as classifier to construct the iEnhancer-RD calculation method for enhancer identification. It is a two-layer classification architecture in which the first layer(layer I) identifies enhancers from a set of DNA sequences, and the second layer(layer II) divides the identified enhancers into two subgroups, namely strong and weak enhancers. Independent dataset test indicates that the proposed method is significantly better than most existing methods, and attains the accuracy of 78.8% and 70.5% in the two layers, respectively. Our iEnhancer-RD architecture is implemented in Python and is available at https://github.com/YangHuan639/iEnhancer-RD.