OE Matching Algorithm for Searching Biological Sequences

Abstract

String matching algorithms play a key role in many computer science problems, and in the implementation of computer software. This problem has received, and continues to receive a great deal of attention due to various applications in text manipulation, information retrieval, speech recognition, image and signal processing and computational biology. In this study, we propose a new algorithm called the Odd and Even algorithm (OE). OE combines an enhanced preprocessing phase from the Berry Ravindran algorithm with our proposed new searching phase procedure. This variety of searching order allows our proposed algorithm to reduce the number of comparison characters and enhances the searching response time. Experimental results show that OE algorithm offers a smaller number of comparisons and offers improved elapsed searching time when compared to other well-known algorithms for searching any length of alphabets and patterns. The proposed algorithm is applicable to searching protein sequence databases as well as any other string searching applications