ABSTRACT

DNA Pattern matching, the problem of finding sub sequences within a long DNA sequence has many applications in computational biology. As the sequences can be long, matching can be an expensive operation, especially as approximate matching is allowed. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Skip Search Multiple Pattern matching algorithm (ISMPM), for DNA sequences. Our approach avoids unnecessary comparisons in the DNA sequence due to this, the number of comparisons gradually decreases and comparison per character ratio of the proposed algorithm reduces accordingly when compared to other existing popular methods. Our experimental results show that there is considerable amount of performance improvement. The total no of comparisons are drastically reduced when the length of the pattern increases in our algorithm.