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Efficient Prediction of DNA-Binding Proteins Using Machine Learning

DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many types of cellular activities. In this paper we describe machine learning systems for the prediction of DNA- binding proteins where a Support Vector Machine and a Cascade Correlation Neural Network are optimized and then compared to determine the learning algorithm that achieves the best prediction performance. The information used for classification is derived from characteristics that include overall charge, patch size and amino acids composition. In total 121 DNA- binding proteins and 238 non-binding proteins are used to build and evaluate the system. For SVM using the ANOVA Kernel with Jack-knife evaluation, an accuracy of 86.7% has been achieved with 91.1% for sensitivity and 85.3% for specificity. For CCNN optimized over the entire dataset with Jack knife evaluation we report an accuracy of 75.4%, while the values of specificity and sensitivity achieved were 72.3% and 82.6%, respectively.