The Prague Stringology Conference 2005

Szymon Grabowski, Veli Makinen, Gonzalo Navarro and Alejandro Salinger

A Simple Alphabet-Independent FM-Index

Abstract:
We design a succinct full-text index based on the idea of Huffman-compressing the text and then applying the Burrows-Wheeler transform over it. The resulting structure can be searched as an FM-index, with the benefit of removing the sharp dependence on the alphabet size, σ, present in that structure. On a text of length n with zero-order entropy H0, our index needs O(n(H0+1)) bits of space, without any dependence on σ. The average search time for a pattern of length m is O(m(H0+1)), under reasonable assumptions. Each position of a text occurrence can be reported in worst case time O((H0+1) log n), while any text substring of length L can be retrieved in O((H0+1)L) average time in addition to the previous worst case time. Our index provides a relevant space/time tradeoff between existing succinct data structures, with the additional interest of being easy to implement. Our experimental results show that, although not among the most succinct, our index is faster than the others in many aspects, even letting them use significatively more space.

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