The Prague Stringology Conference 2006

Rafał Przywarski, Szymon Grabowski, Gonzalo Navarro and Alejandro Salinger

FM-KZ: An Even Simpler Alphabet-Independent FM-Index

In an earlier work [GMN04] we presented a simple FM-index variant, based on the idea of Huffman-compressing the text and then applying the Burrows-Wheeler transform over it. The main drawback of using Huffman was its lack of synchronizing properties, forcing us to supply another bit stream indicating the Huffman codeword boundaries. In this way, the resulting index needed O(n(H0+1)) bits of space but with the constant 2 (concerning the main term). There are several options aiming to mitigate the overhead in space, with various effects on the query handling speed. In this work we propose Kautz-Zeckendorf coding as a both simple and practical replacement for Huffman. We dub the new index FM-KZ. We also present an efficient implementation of the rank operation, which is the main building brick of the FM-KZ. Experimental results show that our index provides an attractive space/time tradeoff in comparison with existing succinct data structures, and in the DNA test it even wins both in search time and space use. An additional asset of our solution is its relative simplicity.

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