Fast low-level pattern matching algorithm

11/18/2016

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by   Janja Paliska Soldo, et al.

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This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern lengths, due to computing precision problem. Our approach successfully deals with large patterns, due to our implementation that uses modular arithmetic. In order to get the results very fast, the code was adapted for multithreading and parallel implementations. The method is reduced to assembly language level instructions, thus the final result shows significant time and memory savings compared to the reference algorithm.