Optimized numerical mapping scheme for filter-based exon location in DNA using a quasi-Newton algorithm

An optimized numerical mapping scheme for achieving improved location of exons in DNA sequences using digital filters is proposed. Characteristic numerical values for the four nucleotides, referred to as pseudo-EIIP values, are obtained using a training procedure where the location accuracy is maximized using a quasi-Newton algorithm based on the Broyden-Fletcher-Goldfarb-Shanno updating formula. A training set of 80 DNA sequences is chosen from the HMR195 database. The objective function for the optimization procedure is formulated using the so-called receiver operating characteristic (ROC) technique and the procedure is initialized using electron-ion interaction potential (EIIP) values. Unbiased testing of the optimized characteristic values is carried out using a set of DNA sequences that has no overlap with the training set. Simulation results show that the pseudo-EIIP values yield more accurate exon locations than those obtained using the actual EIIP values.