Sensitivity Enhancement of DWT Based Algorithm for Detection of CpG Islands in DNA Sequences

Abstract

CpG Islands in DNA sequences play a very important role as gene markers, these are associated with some human malignancies, and also these are useful in the identification of promoter regions. The performance of an algorithm to detect the CpG Islands may be affected by the choice of a particular numerical mapping method. Due to the importance of numerical mapping to convert the nucleotides of DNA sequence to numerical values, it is essential to analyze the performance of various mapping schemes for the detection of CpG Islands in DNA sequences. Hence, in this paper the performance of Discrete Wavelet Transform based algorithm for the detection of CpG Islands in DNA sequences has been studied using existing numerical mapping schemes and its sensitivity has also been enhanced using 24 combinations of integer mapping scheme. The experiment has been done on 30 DNA sequences which are downloaded from National Center for Biotechnology Information. The performance parameters considered in the paper for evaluation purpose are sensitivity, specificity, and accuracy. The results obtained show that the proposed approach of combination of 24 mapping scheme of integer mapping outperforms in terms of sensitivity at different thresholds.