SpliceCombo: A hybrid technique efficiently use for principal component analysis of splice site prediction

Abstract

The primary step in search of the gene prediction is an identification of the coding region from genomic DNA sequence. Gene structure in the case of a eukaryotic organism is composed of promoter, intron, start codon, exons, stop codon, etc. Splice site prediction, which separates the junction between exon and intron, though the sequence beside. The splice sites have huge preservation; however, the precision of the tool exhibits less than 90 %. The main objective of this work to exhibits a hybrid technique that efficiently improves the existing gene recognition technique. Therefore, to enhance the identification of splice sites, the respective algorithm needs to be improved. Our proposed method, ‘SpliceCombo’ involves three stages. At initial stage, which considers the principal Component Analysis, based on the feature extracted. In the intermediate stage, i.e., the second stage Case- Based Reasoning is done, i.e., feature selection. The third stage uses support vector machine based along with polynomial kernel function for final classification. In comparison with other methods, the proposed SpliceCombo model outperforms other prediction models with respect to prediction accuracies. Particularly for donor splice site the methodology exhibits sensitivity is 97.25 % accurate and specificity is 97.46 % accurate. For acceptor Splice Site the sensitivity is 96.51 % and Specificity is 94.48 % correct