Improved Algorithms for Finding Consistent Superstrings Based on a New Graph Model

  • Authors:

  • Jin Wook Kim;Siwon Choi;Joong Chae Na;Jeong Seop Sim

  • Affiliations:

  • School of Computer and Information Engineering, Inha University, Incheon, Korea 402-751;School of Computer and Information Engineering, Inha University, Incheon, Korea 402-751;Department of Computer Science and Engineering, Sejong University, Seoul, Korea 143-747;School of Computer and Information Engineering, Inha University, Incheon, Korea 402-751

  • Venue:
  • ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
  • Year:
  • 2009

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Abstract

The problems that are related to string inclusion and non-inclusion have been vigorously studied in such diverse fields as data compression, molecular biology, and computer security. Given a finite set of negative strings 驴 and a finite set of positive strings 驴, a string 驴 is a consistent superstring if every positive string is a substring of 驴 and no negative string is a substring of 驴. The shortest (resp. longest) consistent superstring problem is finding a string 驴 that is the shortest (resp. longest) among all the consistent superstrings for the given sets of strings.In this paper, we first propose a new graph model based on the Aho-Corasick algorithm to represent the consistent superstrings for the given sets. Then, we propose improved algorithms for the problems of the shortest consistent superstring and the longest consistent superstring using the graph model.