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

Authors:
Loris Nanni;Alessandra Lumini
Affiliations:
DEIS, IEIIT - CNR, Universití di Bologna, Viale Risorgimento 2, 40136 Bolonga, Italy;DEIS, IEIIT - CNR, Universití di Bologna, Viale Risorgimento 2, 40136 Bolonga, Italy
Venue:
Expert Systems with Applications: An International Journal
Year:
2008

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Abstract

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.