The functional annotation of amino acid sequences is one of the most important problems in bioinformatics. Different programs have been successfully applied for recognition of some functional classes; nevertheless, many functional groups still cannot be predicted with the required accuracy. We developed a new method for protein function recognition using the original approach of sequence description. Each sequence of the training set is compared with the query sequence, and the local similarity scores are calculated for the query sequence positions and used as input data for the original classifier. The method was tested using leave-one-out cross-validation for three data sets covering 58 enzyme classes. Two tested sets including noncrossing functional classes were recognized with high accuracy at various levels of classification hierarchy. The majority of these classes were predicted with 100% accuracy, showing a зrediction ability comparable with the HMMer method and an accuracy superior to the SVM-Prot program. When the tested set was composed of intersected classes of ligand specificity, the prediction accuracy was less; however, the accuracy increased as the size of the predicted class expanded. The proposed method can be used for both predicting protein functional class and selecting the functionally significant sites in a sequence.
J. Bioinform. Computat. Biol., 2008, 6 (4), 709-725.