Compressed suffix array

Article summary

In computer science, a compressed suffix array is a compressed data structure for pattern matching. Compressed suffix arrays are a general class of data structure that improve on the suffix array. These data structures enable quick search for an arbitrary string with a comparatively small index. Given a text T of n characters from an alphabet Σ, a compressed suffix array supports searching for arbitrary patterns in T. For an input pattern P of m characters, the search time is typically O(m) or O(m + log(n)). The space used is typically O(n H_k(T)) + o(n) , where H_k(T) is the k-th order empirical entropy of the text T. The time and space to construct a compressed suffix array are normally . The original presentation of a compressed suffix array solved a long-standing open problem by showing that fast pattern matching was possible using only a linear-space data structure, namely, one proportional to the size of the text T, which takes O(n \, {\log |\Sigma|}) bits. The conventional suffix array and suffix tree use \Omega(n \, {\log n}) bits, which is substantially larger. The basis for the data structure is a recursive decomposition using the "neighbor function," which allows a suffix array to be represented by one of half its length. The construction is repeated multiple times until the resulting suffix array uses a linear number of bits.…

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