Protein sequence classification involves feature selection for accurate classification. Popular protein sequence classification techniques involve extraction of specific features from the sequences. Researchers apply some well-known classification techniques like neural networks, Genetic algorithm, Fuzzy ARTMAP, Rough Set Classifier etc for accurate classification. This paper presents a review is with three different classification models such as neural network model, fuzzy ARTMAP model and Rough set classifier model. This is followed by a new technique for classifying protein sequences. The proposed model is typically implemented with an own designed tool and tries to reduce the computational overheads encountered by earlier approaches and increase the accuracy of classification.