An Improved Fast Search Method Using Histogram Features for DNA Sequence Database

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.

Authors:

• Qiu Chen
• Feifei Lee
• Koji Kotani
• Tadahiro Ohmi

Keywords:

• Fast search
• DNA sequence
• Histogram feature
• Smith-Waterman algorithm
• Local search

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