1. A method of classifying substructures of at least one unmarked string using at least one training data set, comprising the steps of: constructing a model of class labels and substructures within strings of the at least one training data set, wherein the training data set has markers identifying labeled substructures; inserting markers in the at least one unmarked string in accordance with the model, wherein the markers identify substructures in the at least one unmarked string similar to substructures within strings of the at least one training data set; and predicting class labels of substructures in the at least one unmarked string similar to substructures within strings of the at least one training data set in accordance with the model.