Abstract: In this paper, we propose an efficient hierarchical DNA
sequence search method to improve the search speed while the
accuracy is being kept constant. For a given query DNA sequence,
firstly, a fast local search method using histogram features is used as a
filtering mechanism before scanning the sequences in the database.
An overlapping processing is newly added to improve the robustness
of the algorithm. A large number of DNA sequences with low
similarity will be excluded for latter searching. The Smith-Waterman
algorithm is then applied to each remainder sequences. Experimental
results using GenBank sequence data show the proposed method
combining histogram information and Smith-Waterman algorithm is
more efficient for DNA sequence search.