Question: Suffix Array Vs. Compressed Suffix Array Vs. Bwt Search
gravatar for Rob
6.9 years ago by
United States
Rob4.5k wrote:

Hi all,

I was wondering if there is a good reference on what the (practically) fastest data structure for exact sequence search is. Specifically, I'm curious about the speed of finding all occurrences (exactly) of a string in a large corpus using backward search in a BWT versus search in a (presumably uncompressed) suffix array. I understand that they can both be performed asymptotically in O(m), where m is the length of the pattern string, with both structures. However, I'm curious if there are significant practical differences in the search speed. Any references or benchmarks would be greatly appreciated.



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