Filter-based methodology for the location of hot spots in proteins and exons in DNA

The so-called receiver operating characteristic technique is used as a tool in an optimization procedure for the improvement and assessment of a filter-based methodology for the location of hot spots in protein sequences and exons in DNA sequences. By optimizing the characteristic values of the nucleotides, high efficiency as well as improved accuracy can be achieved relative to results obtained with the electron-ion interaction potentials. On the other hand, by using the proposed filter-based methodology with binary sequences, improved accuracy can be achieved although the efficiency is somewhat compromised relative to that achieved using the optimized characteristic values. Extensive experimental results, evaluated using measures such as the g-mean, the Matthews correlation coefficient, and the chi-square statistic, show that the filter-based methodology performs much better than existing techniques using the short-time discrete Fourier transform, particularly in applications where short exons are involved.