Why it matters

Suffix arrays enable fast substring queries. Foundation of bioinformatics.

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The architecture

Sort all suffixes.

SA-IS or DC3 for linear.

LCP array for extras.

Suffix array structureSort suffixesO(n log n) or O(n)LCP arrayfor enhancedSubstring searchO(m log n)SA-IS (Nong et al. 2011) linear time; bioinformatics workhorse
Suffix array structure.
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How it works end to end

SA-IS Nong 2011.

DC3 Karkkainen.

LCP array.