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利用水平分割法计算给定串中的所有Maximal(NE/SNE) Repeats 被引量:1

Compute All Maximal(NE/SNE) Repeats in a String with Horizontal-division Method
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摘要 提出一种利用给定符号串x[1…n]的后缀数组和最长公共前缀数组求x所有最大重复的新方法水平分割法.通过对x的最大不可扩展重复和最大超级不可扩展重复所有可能出现的位置以及判定条件的提炼,分别给出仅由x的后缀数组和最长公共前缀数组求x的所有最大重复、最大不可扩展重复和最大超级不可扩展重复的算法.该算法克服了除后缀数组和最长公共前缀数组外,还需利用其他辅助数组的缺陷,降低了空间开销,且时间复杂度没有增加,并可以在对最长公共前缀数组仅进行一次扫描的情况下求出给定串的所有最大重复、最大不可扩展重复和最大超级不可扩展重复. We proposed a new method-horizontal-division method by which we can compute all the Maximal Repeats of string x using only suffix array SAx and LCP array LCPx. We analyzed the situations and locations where the Maximal NE-Repeats and SNE-Repeats of x can be. Then we designed three algorithms by which all Maximal Repeats, Maximal NE-Repeats, and Maximal SNE-Repeats in a string x [1…n] can be computed only by means of SAx and LCPx. The given algorithms overcome the defects of the corresponding algorithms which require other assistant arrays in addition to suffix array and LCP array. So our algorithms reduce the space requirement greatly. Moreover, the time complexity of these algorithms is not increased. In addition, we can get all the Maximal Repeats, Maximal NE Repeats and Maximal SNE Repeats of a string by only scanning LCP array once.
出处 《吉林大学学报(理学版)》 CAS CSCD 北大核心 2008年第5期915-924,共10页 Journal of Jilin University:Science Edition
基金 国家自然科学基金(批准号:60373097)
关键词 重复(子串) 后缀数组 水平分割法 repeats suffix array horizonta-division method
作者简介 袁哲(1984-),男,汉族,硕士研究生,从事信息安全和密码系统的研究,E-mail:iamyuanzhe@163.com 联系人:赵永哲(1961-),男,汉族,博士,教授,从事信息安全和密码系统的研究,E-mail:yongzhe@jlu.edu.cn.
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  • 1Lander E S, Linton L M, Birren B, et al. Initial Sequencing and Analysis of the Human Genome [ J]. Nature, 2001, 409 : 860-921.
  • 2Kurtz S, Choudhuri J V, Ohlebusch E, et al. The Manifold Applications of Repeat Analysis on a Genomic Scale [ J ]. Nucl Acids Res, 2001, 29(22): 4633-4642.
  • 3Delcher A L, Kasif S, Fleischmann R D, et al. Alignment of Whole Genomes [ J ]. Nucl Acids Res, 1999, 27 ( 11 ) : 2369-2376.
  • 4Manzini G. An Analysis of the Burrows-Wheeler Transform [J]. Journal of the ACM, 2001,48(3) : 407-430.
  • 5Zamir O, Etrioni O. A Dynamic Clustering Interface to Web Search Results [J]. Computer Networks, 1999, 31(11/16) : 1361-1374.
  • 6Franek F, Smyth W F, TANG Yu-dong. Computing All Repeats Using Suffix Arrays [ J ]. Journal of Automata, Languages & Combinatorics, 2003, 8(4): 579-591.
  • 7btcCreight E M. A Space-economical Suffix Tree Construction Algorithm [ J]. Assoc Comput Math, 1976, 23(2): 262-272.
  • 8Crochmore M. An Optimal Algorithm for Computing the Repetition in a Word [J]. IPL, 1981, 12(5) : 244-250.
  • 9Main M G, Lorentz R J. An O ( nlog n) Algorithm for Finding M1 Repetitions in a String [ J ]. Algs, 1984, 5 (3) : 422-432.
  • 10Abouelhoda M I, Kurtz S, Ohlebusch E. Replacing Suffix Trees with Enhanced Suffix Arrays [ J ]. Journal of Discrete Algs, 2004, 2(1) : 53-86.

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