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A fast algorithm for making suffix arrays and for Burrows-Wheeler transformation

机译:制作后缀数组和Burrows-Wheeler变换的快速算法

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We propose a fast and memory efficient algorithm for sorting suffixes of a text in lexicographic order. It is important to sort suffixes because an array of indexes of suffixes is called a suffix array and it is a memory efficient alternative of the suffix tree. Sorting suffixes is also used for the Burrows-Wheeler (see Technical Report 124, Digital SRC Research Report, 1994) transformation in the block sorting text compression, therefore fast sorting algorithms are desired. We compare algorithms for making suffix arrays of Bentley-Sedgewick (see Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms, p.360-9, 1997), Andersson-Nilsson (see 35th Symp. on Foundations of Computer Science, p.714-21, 1994) and Karp-Miller-Rosenberg (1972) and making suffix trees of Larsson (see Data Compression Conference, p.190-9, 1996) on the speed and required memory and propose a new algorithm which is fast and memory efficient by combining them. We also define a measure of difficulty of sorting suffixes: average match length. Our algorithm is effective when the average match length of a text is large, especially for large databases.
机译:我们提出了一种快速且高效存储的算法,用于按字典顺序对文本的后缀进行排序。对后缀进行排序很重要,因为后缀索引数组称为后缀数组,它是后缀树的内存有效替代方法。排序后缀还用于块排序文本压缩中的Burrows-Wheeler(请参阅技术报告124,Digital SRC研究报告,1994)转换,因此需要快速的排序算法。我们比较了制作Bentley-Sedgewick后缀数组的算法(请参阅第8届ACM-SIAM离散算法研讨会论文集,第360-9页,1997年),Andersson-Nilsson(请参阅第35届计算机科学基础Symp。)。 .714-21,1994)和Karp-Miller-Rosenberg(1972)并根据速度和所需的内存制作Larsson的后缀树(请参见Data Compression Conference,p.190-9,1996),并提出了一种新的算法,该算法速度很快通过将它们结合起来,可以提高存储效率。我们还定义了排序后缀的难度的度量:平均匹配长度。当文本的平均匹配长度很大时,特别是对于大型数据库,我们的算法有效。

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