An Approach to Find Proper Execution Parameters of n-Gram Encoding Method Based on Protein Sequence Classification

Abstract

Various protein sequence classification approaches are developed to classify unknown sequences in to its classes or familes with an certain accuracy. Features extraction from protein sequence is a key technique to implement all approaches. N-gram encoding method is a popular feature extraction procedure. But to maintain the low computational time and high accuracy level of classification, it requires to fix up the upper limit of ‘N’ of N-gram encoding method. On the other hand, the standard deviation value of protein sequence is one of the important feature value which is extracted by N-gram encoding method. This feature can be extracted by two different ways like standard deviation calculation using standard mean value and using floating mean value. It is also important to find proper method to calculate the value of standard deviation. In this paper, an investigational proof has done to find upper limit of N-gram encoding method as well as find the proper technique to calculate the standard deviation value as a feature which are extracted from unknown protein sequence.