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arXiv · 1103.2613

Linear pattern matching on sparse suffix trees

Roman Kolpakov·Gregory Kucherov·Tatiana Starikovskaya
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Abstract

Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse suffix tree} \cite{KU-96} with appropriately defined suffix links. Assuming, under the standard unit-cost RAM model, that a word can store up to $\log_σn$ characters ($σ$ the alphabet size), our index takes $O(n/\log_σn)$ space, i.e. the same space as the packed string itself. The resulting pattern matching algorithm runs in time $O(m+r^2+r\cdot occ)$, where $m$ is the length of the pattern, $r$ is the actual number of characters stored in a word and $occ$ is the number of pattern occurrences.

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Roman Kolpakov, Gregory Kucherov, Tatiana Starikovskaya. 2011-03-14. Linear pattern matching on sparse suffix trees. https://doi.org/10.1109/ccp.2011.45

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