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Engineering a compressed suffix tree implementation
2009
ACM Journal of Experimental Algorithmics
Suffix tree is one of the most important data structures in string algorithms and biological sequence analysis. Unfortunately, when it comes to implementing those algorithms and applying them to real genomic sequences, often the main memory size becomes the bottleneck. This is easily explained by the fact that while a DNA sequence of length n from alphabet Σ = {A, C, G, T } can be stored in n log |Σ| = 2n bits, its suffix tree occupies O(n log n) bits. In practice, the size difference easily
doi:10.1145/1498698.1594228
fatcat:7lbrz6keync55ic54a35cha6uq