Reversals and transpositions over finite alphabets

被引:34
|
作者
Radcliffe, AJ [1 ]
Scott, AD
Wilmer, EL
机构
[1] Univ Nebraska, Dept Math, Lincoln, NE 68588 USA
[2] UCL, Dept Math, London WC1E 6BT, England
[3] Oberlin Coll, Dept Math, Oberlin, OH 44074 USA
关键词
strings; sorting; genome comparison; reversals; transpositions; NP-complete problems; MAX-SNP hardness; approximation algorithms;
D O I
10.1137/S0895480103433550
中图分类号
O29 [应用数学];
学科分类号
070104 ;
摘要
Extending results of Christie and Irving, we examine the action of reversals and transpositions on finite strings over an alphabet of size k. We show that determining reversal, transposition, or signed reversal distance between two strings over a finite alphabet is NP-hard, while for "dense" instances we give a polynomial-time approximation scheme. We also give a number of extremal results, as well as investigating the distance between random strings and the problem of sorting a string over a finite alphabet.
引用
收藏
页码:224 / 244
页数:21
相关论文
共 50 条
  • [21] Genome Rearrangement Distance with Reversals, Transpositions, and Indels
    Alexandrino, Alexsandro Oliveira
    Oliveira, Andre Rodrigues
    Dias, Ulisses
    Dias, Zanoni
    JOURNAL OF COMPUTATIONAL BIOLOGY, 2021, 28 (03) : 235 - 247
  • [22] Finding optimal finite biological sequences over finite alphabets: the OptiFin toolbox
    Garnier, Regis
    Guyeux, Christophe
    Chretien, Stephane
    2017 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (CIBCB), 2017, : 225 - 233
  • [23] Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem
    Brito, Klairton Lima
    Oliveira, Andre Rodrigues
    Dias, Ulisses
    Dias, Zanoni
    ALGORITHMS FOR COMPUTATIONAL BIOLOGY (ALCOB 2018), 2018, 10849 : 65 - 75
  • [24] Sorting Unsigned Permutations by Weighted Reversals, Transpositions, and Transreversals
    Lou, Xiao-Wen
    Zhu, Da-Ming
    JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY, 2010, 25 (04) : 853 - 863
  • [25] On Finite Memory Observability of a Class of Systems Over Finite Alphabets with Linear Dynamics
    Fan, Donglei
    Tarraf, Danielle C.
    2014 IEEE 53RD ANNUAL CONFERENCE ON DECISION AND CONTROL (CDC), 2014, : 3884 - 3891
  • [26] Real-Time Indexing over Fixed Finite Alphabets
    Amir, Amihood
    Nor, Igor
    PROCEEDINGS OF THE NINETEENTH ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 2008, : 1086 - 1095
  • [27] Compositional Analysis of Hybrid Systems Defined Over Finite Alphabets
    Cubuktepe, Murat
    Ahmadi, Mohamadreza
    Topcu, Ufuk
    Hencey, Brandon
    IFAC PAPERSONLINE, 2018, 51 (16): : 115 - 120
  • [28] Sorting Unsigned Permutations by Weighted Reversals,Transpositions,and Transreversals
    娄晓文
    朱大铭
    Journal of Computer Science & Technology, 2010, 25 (04) : 853 - 863
  • [29] Sorting Permutations by Prefix and Suffix Versions of Reversals and Transpositions
    Lintzmayer, Carla Negri
    Dias, Zanoni
    LATIN 2014: THEORETICAL INFORMATICS, 2014, 8392 : 671 - 682
  • [30] Signed genome rearrangement by reversals and transpositions: models and approximations
    Lin, GH
    Xue, GL
    THEORETICAL COMPUTER SCIENCE, 2001, 259 (1-2) : 513 - 531