Multithreaded KMP: A Proposed DNA Sequencing Algorithm
DNA sequencing is the process of decoding the nucleotide bases in a DNA molecule. The advent of DNA
sequencing has significantly accelerated biological research and discovery. There are a number of string searching
algorithms as well which are widely used for DNA sequencing namely Knuth-Morris- Pratt (KMP), Boyer Moore, Rabin-
Karp, Longest Common Subsequence Problem etc. In this paper a multithreaded KMP algorithm is proposed for DNA
sequencing. This work primarily aims at reducing the pattern searching time of the original KMP algorithm by using the
concepts of divide and conquer and parallel processing techniques and also enables it to make a search on all the available
matches of the source DNA thereby increasing its flexibility.
Keywords- KMP Algorithm, DNA Sequencing, Alignment, String Matching, Time.