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arXiv · 1703.02224

Space-efficient K-MER algorithm for generalized suffix tree

Freeson Kaniwa·Venu Madhav Kuthadi·Otlhapile Dinakenyane·Heiko Schroeder
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Abstract

Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory efficient algorithm of a generalized suffix tree which reduces the space size by a factor of 10 when the size of the pattern is known beforehand. Experiments on the chromosomes and Pizza&Chili corpus show significant advantages of our algorithm over standard linear time suffix tree construction in terms of memory usage for pattern searching.

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Freeson Kaniwa, Venu Madhav Kuthadi, Otlhapile Dinakenyane, Heiko Schroeder. 2017-03-07. Space-efficient K-MER algorithm for generalized suffix tree. https://arxiv.org/abs/1703.02224

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