Browse > Article
http://dx.doi.org/10.3745/KIPSTA.2009.16A.5.319

Constant Time RMESH Algorithm for Computing Longest Common Substring and Maximal Repeat of String  

Han, Seon-Mi (단국대학교 컴퓨터과학)
Woo, Jin-Woon (단국대학교 컴퓨터학부)
Publication Information
The KIPS Transactions:PartA / v.16A, no.5, 2009 , pp. 319-326 More about this Journal
Abstract
Since string operations were applied to computational biology area, various data structures and algorithms for computing efficient string operations have been studied. The longest common substring problem is an operation to find the longest matching substring in more than two strings, and maximal repeat of string problem is an operation to find substrings repeated more than once in the given string. These operations are importantly used in the string processing area such as pattern matching and likelihood measurement. In this paper, we present algorithms to compute the longest common substring of two strings and to find the maximal repeat of string using three-dimensional $n{\times}n{\times}n$ processors on RMESH(Reconfigurable MESH). Our algorithms have O(1) time complexity.
Keywords
String; Longest Common Substring; Maximal Repeat; RMESH;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 W. Masek and M. Paterson, "A fast algorithm computing string edit distances," J. of Computer and System Sciences, 20(1), pp.13-31, 1980.   DOI   ScienceOn
2 전정은, 박희진, 김동규, "써픽스 배열을 이용한 최장 공통 부분 스트링 계산," 한국정보과학회 가을 학술발표논문집, Vol.4, No.2, pp.739-741, 2004.   과학기술학회마을
3 I. Lee, C. Illiopoulos, K. Park, "Linear time algorithm for the longest common repeat problem," J. of Discrete Algorithms, 5, pp.243-249, 2006.   DOI   ScienceOn
4 김기원, 우진운, "선형 사진트리로 표현된 이진 영상의 면적과 둘레 길이를 계산하기 위한 상수시간 RMESH," 한국정보처리 학회 논문지, 제5권, 제7호, pp.1746-1758, 1998.   과학기술학회마을
5 Y. Jiang, A. Wright, "O(k) parallel algorithms for approximate string matching," Neurla, Parallel and Scientific Computations, Vol.1, pp.443-452, 1993.
6 J. Jang, H. Park, and V. Prasanna, "A Fast Algorithm for Computing Histogram on a Reconfigurable Mesh," IEEE Trans. on Pattern Analysis and Machine Intelligence, Vol.17, No.2, pp.97-106, 1995.   DOI   ScienceOn
7 R. A. Wagner, Michael J. Fischer, "The String-to-String Correction Problem," Journal of the ACM (JACM), Vol.21, Issue 1, pp.168-173, 1974.   DOI   ScienceOn
8 Dan. Gusfield, Algorithms on Strings, Trees, and Sequences, Computer Science and Computational Biology, CamBridge University Press, 1997.
9 A. Apostolico, C. Iliopoulos, G. Landau, BSchieber, and U. Vishkin, "Parallel Construction of a Suffix Tree with Application," Algorithmica, Vol.3, pp.347-365, 1988.   DOI
10 G. Landau, U. Vishkin, "Fast parallel and serial approximate string matching," J. of Algorithms, Vol.10, pp.157-169, 1989.   DOI
11 A. Datta, S. Subbiah, "Constant Time Algorithms for String Processing on the Reconfigurable Mesh," The 4th Australasian conference on Parallel and real-time systems, pp.226-237, 1997.
12 R. Miller, V. Prasanna-Kumar, D. Reisis, and Q. Stout, "Parallel Computation on Reconfigurable Meshes," IEEE Transactions on Computers, Vol.42, No.6, pp.678-692, 1993.   DOI   ScienceOn
13 Y. Ben-Asher, D. Peleg, R. Ramaswami, and A. Schuster, "The Power of Reconfiguration," Journal of Parallel and Distributed Computing, 13, pp.139-153, 1991.   DOI   ScienceOn
14 S. Needleman, C. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins," J. Mol. BioInformatics, 48(3), 443-453, 1970.   DOI
15 Z. Galil, "A Constant Time Optimal Parallel String Matching Algorithm," J. of ACM, Vol.42, pp.908-918, 1995.   DOI   ScienceOn
16 H. Lee, F. Ercal, "RMESH Algorithms for Parallel String Matching," International Symposium on Parallel Architectures, Algorithms and Networks, pp.223-226, 1997
17 M. Nigam and S. Sahni, "Sorting n Numbers On n×n Reconfigurable Meshes With Buses," Proceedings 7th International Parallel Processing Symposium, pp.174-181, 1993.   DOI   ScienceOn
18 김경훈, 우진운, "RMESH 구조에서 unaligned 선형사진트리 의 alignment를 위한 상수시간 알고리즘," 정보과학회논문지, 제31권 1,2호, pp.10-18, 2004.   과학기술학회마을