Locally Compressed Suffix Arrays

Compressed Spaced Suffix Arrays

Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA). In this paper we show how to compress SSAs relative to normal suffix arrays (SAs) and still su...

Compressed Suffix Arrays for Massive Data

We present a fast space-efficient algorithm for constructing compressed suffix arrays (CSA). The algorithm requires O(n logn) time in the worst case, and only O(n) bits of extra space in addition to the CSA. As the basic step, we describe an algorithm for merging two CSAs. We show that the construction algorithm can be parallelized in a symmetric multiprocessor system, and discuss the possibili...

A Simple Introduction to Compressed Suffix Arrays

This document attempts to provide a simple introduction to a quite fun, and possibly-becominguseful full-text index structure: The compressed suffix array. I have tried to write this document so that it’s accessible to a reader with a comfortable grasp of advanced undergraduate computer science concepts in both theory and systems. Please let me know if that’s not the case.

Algorithms on Strings based on the Compressed Suffix Arrays

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Broadword Computing and Fibonacci Code Speed Up Compressed Suffix Arrays