Analysis of binary feature mapping rules for promoter recognition in imbalanced DNA sequence datasets using Support Vector Machine

Recognition of specific functionally-important DNA sequence fragments is considered one of the most important problems in bioinformatics. One type of such fragments are promoters, i.e., short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. In this paper, a machine learning method, called support vector machine (SVM), is used for classification of DNA sequences and promoter recognition. For optimal classification, 11 rules for mapping of DNA sequences into binary SVM feature space are analyzed. Classification is performed using a power series kernel function. Kernel parameters are optimized using a modification of the Nelder-Mead (downhill simplex) optimization method. The results of classification for drosophila and human sequence datasets are presented.