Generalized Needleman–Wunsch algorithm for the recognition of T-cell epitopes

In this paper, we propose a new encoding technique that combines the different physicochemical properties of amino acids together with Needleman–Wunsch algorithm. The algorithm was tested in the recognition of T-cell epitopes. A series of SVM classifiers, where each SVM is trained using a different physicochemical property, combined with the “max rule” enables us to obtain an improvement over the state-of-the-art approaches.