English

Space-efficient K-MER algorithm for generalized suffix tree

Data Structures and Algorithms 2017-03-08 v1

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.

Keywords

Cite

@article{arxiv.1703.02224,
  title  = {Space-efficient K-MER algorithm for generalized suffix tree},
  author = {Freeson Kaniwa and Venu Madhav Kuthadi and Otlhapile Dinakenyane and Heiko Schroeder},
  journal= {arXiv preprint arXiv:1703.02224},
  year   = {2017}
}

Comments

10 pages

R2 v1 2026-06-22T18:38:00.485Z