In recent years we have witnessed an exponential increase in the amount of biological information, either DNA or protein sequences, that has become available in public databases. This has been followed by an increased interest in developing computational techniques to automatically classify these large volumes of sequence data into various categories corresponding to either their role in the chromosomes, their structure, and/or their function. In this paper we evaluate some of the widely-used sequence classification algorithms and develop a framework for modeling sequences in a fashion so that traditional machine learning algorithms, such as support vector machines, can be applied easily. Our detailed experimental evaluation shows that the SVM-based approaches are able to achieve higher classification accuracy compared to the more traditional sequence classification algorithms such as Markov model based techniques and K-nearest neighbor based approaches.
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