The Prague Stringology Conference 2001

Thomas Berry, S. Keller and S. Ravindran

Searching in an Efficiently Stored DNA Text Using a Hardware Solution

Abstract:
In this paper, we describe a storage method that reduces the size of a DNA text file to 25% of its original size. Also outlined is a new algorithm, which can search an input stream of DNA text for multiple DNA sub-strings in a single pass. Although this new algorithm is competitive when compared to the majority of existing string matching algorithms, the intention is to further improve performance by implementing the algorithm as a hardware-only solution.

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