New Techniques for the Location of Hot Spots in Proteins and Exons in DNA Using Digital Filters

The development, implementation, and performance evaluation of new techniques for the location of hot spots in proteins and exons in DNA using digital filters are presented. The application of bandpass notch (BPN) digital filters for locating hot spots in proteins is first investigated. A technique is proposed for designing the appropriate BPN filter for a specific protein sequence in which the area under the amplitude response is minimized to achieve maximum selectivity for a chosen stability margin. The minimization is performed using the golden-section search. A tuning technique is also proposed for improving the accuracy of the BPN filter. The tuning is carried out using a least-squares polynomial model. Several example protein sequences are used to illustrate these techniques. BPN filters are then employed for locating exons in DNA. An additional step of lowpass filtering is introduced in order to detect the strength of the bandpass filtered signal as a function of nucleotide location. For the character-to-numerical mapping, the application of the electron-ion interaction potentials (EIIPs) of the nucleotides as well as their binary sequences is investigated.

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