OE Matching Algorithm for Searching Biological Sequences

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.