Phage virion proteins (PVPs) play an important role in the host cell. Fast and accurate identification of PVPs is beneficial for the discovery and development of related drugs. Although wet experimental approaches are the first choice to identify PVPs, they are costly and time-consuming. Thus, researchers have turned their attention to computational models, which can speed up related studies. Therefore, we proposed a novel machine-learning model to identify PVPs in the current study. First, 50 different types of physicochemical properties were used to denote protein sequences. Next, two different approaches, including Pearson's correlation coefficient (PCC) and maximal information coefficient (MIC), were employed to extract discriminative information. Further, to capture the high-order correlation information, we used PCC and MIC once again. After that, we adopted the least absolute shrinkage and selection operator algorithm to select the optimal feature subset. Finally, these chosen features were fed into a support vector machine to discriminate PVPs from phage non-virion proteins. We performed experiments on two different datasets to validate the effectiveness of our proposed method. Experimental results showed a significant improvement in performance compared with state-of-the-art approaches. It indicates that the proposed computational model may become a powerful predictor in identifying PVPs.
Keywords: LASSO; Pearson's correlation coefficient; maximal information coefficient; phage virion proteins; support vector machine.