Optimal suffix tree construction with large alphabets

被引:274
|
作者
Farach, M [1 ]
机构
[1] Rutgers State Univ, Dept Comp Sci, Piscataway, NJ 08855 USA
关键词
D O I
10.1109/SFCS.1997.646102
中图分类号
TP301 [理论、方法];
学科分类号
081202 ;
摘要
The suffix tree of a string is the fundamental data structure of combinatorial pattern matching. Weiner [Wei73] who introduced the data structure, gave an O(n)-time algorithm far building the suffix: tree of an n-character string Brawn from a constant size alphabet. In the comparison model, there is a trivial Omega(n log n)-time lower bound based on sorting, and Weiner's algorithm matches this bound trivially. For integer alphabets, a substantial gap remains between the known upper and lower bounds, and closing this gap is the main open question in the construction of suffix trees. There is no super-linear lower bound, and the fastest known algorithm was the O(n log n) time comparison based algorithm. We settle this open problem by closing the gap: we build suffix trees in linear fine for integer alphabet.
引用
收藏
页码:137 / 143
页数:7
相关论文
共 50 条
  • [31] Space-Efficient Construction Algorithm for the Circular Suffix Tree
    Hon, Wing-Kai
    Ku, Tsung-Han
    Shah, Rahul
    Thankachan, Sharma V.
    COMBINATORIAL PATTERN MATCHING, 2013, 7922 : 142 - 152
  • [32] Space-Efficient Construction Algorithm for the Circular Suffix Tree
    Hon, Wing-Kai
    Ku, Tsung-Han
    Shah, Rahul
    Thankachan, Sharma V.
    2013 DATA COMPRESSION CONFERENCE (DCC), 2013, : 496 - 496
  • [33] MapReduce based Parallel Suffix Tree Construction for Human Genome
    Satish, Umesh Chandra
    Kondikoppa, Praveenkumar
    Park, Seung-Jong
    Patil, Manish
    Shah, Rahul
    2014 20TH IEEE INTERNATIONAL CONFERENCE ON PARALLEL AND DISTRIBUTED SYSTEMS (ICPADS), 2014, : 664 - 670
  • [34] A new compressed suffix tree supporting fast search and its construction algorithm using optimal working space
    Kim, DK
    Park, H
    COMBINATORIAL PATTERN MATCHING, PROCEEDINGS, 2005, 3537 : 33 - 44
  • [35] Parallel construction of large suffix trees on a PC cluster
    Chen, CX
    Schmidt, B
    EURO-PAR 2005 PARALLEL PROCESSING, PROCEEDINGS, 2005, 3648 : 1227 - 1236
  • [36] A simple parallel cartesian tree algorithm and its application to parallel suffix tree construction
    Shun, Julian
    Blelloch, Guy E.
    ACM Transactions on Parallel Computing, 2014, 1 (01)
  • [37] A fast algorithm for constructing suffix arrays for DNA alphabets
    Rabea, Zeinab
    El-Metwally, Sara
    Elmougy, Samir
    Zakaria, Magdi
    JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES, 2022, 34 (07) : 4659 - 4668
  • [38] Suffix cactus: A cross between suffix tree and suffix array
    Karkkainen, J
    COMBINATORIAL PATTERN MATCHING, 1995, 937 : 191 - 204
  • [39] Parallel and private generalized suffix tree construction and query on genomic data
    Md Momin Al Aziz
    Parimala Thulasiraman
    Noman Mohammed
    BMC Genomic Data, 23
  • [40] Efficient construction of minimum-redundancy codes for large alphabets
    Moffat, A
    Turpin, A
    IEEE TRANSACTIONS ON INFORMATION THEORY, 1998, 44 (04) : 1650 - 1657