A Numerical Method for Suffix Array Index Compression

Baomin Xu, Jie Huang, Yang Yang
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Abstract

Suffix arrays is versatile data structures playing a key role in numerous string processing applications such as the data structure can be used to represent the given DNA strings. However, the most serious drawback of suffix arrays is their size, namely space usage. In this paper, we propose a new suffix array compression technique, i.e., numerical method for suffix array index compression, for the problem. With the method, we will translate DNA bases characters ATGC to the corresponding integer number 1234. The experimental results show that the numerical method for suffix array index compression not only can greatly compress the memory space of suffix array, but also can retain the quick search characteristics of suffix array.
后缀数组索引压缩的数值方法
后缀数组是一种通用的数据结构,在许多字符串处理应用程序中起着关键作用,例如该数据结构可用于表示给定的DNA字符串。然而,后缀数组最严重的缺点是它们的大小,即空间使用。针对这一问题,我们提出了一种新的后缀数组压缩技术,即后缀数组索引压缩数值方法。利用该方法,我们将DNA碱基字符ATGC翻译成相应的整数1234。实验结果表明,采用数值方法对后缀数组进行索引压缩,不仅可以大大压缩后缀数组的存储空间,而且可以保持后缀数组的快速搜索特性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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