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arXiv · 1312.3422

Compressed Spaced Suffix Arrays

Travis Gagie·Giovanni Manzini·Daniel Valenzuela
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Abstract

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 support fast random access to them. We first prove a theoretical upper bound on the space needed to store an SSA when we already have the SA. We then present experiments indicating that our approach works even better in practice.

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Travis Gagie, Giovanni Manzini, Daniel Valenzuela. 2013-12-12. Compressed Spaced Suffix Arrays. https://arxiv.org/abs/1312.3422

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