Point matching under non-uniform distortions

  • Authors:
  • Tatsuya Akutsu;Kyotetsu Kanaya;Akira Ohyama;Asao Fujiyama

  • Affiliations:
  • Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan;Department of Bioscience Systems, Mitsui Knowledge Industry Co., Ltd. 2-7-14 Higashinakano, Nakano-ku, Tokyo 164-8555, Japan;Department of Bioscience Systems, Mitsui Knowledge Industry Co., Ltd. 2-7-14 Higashinakano, Nakano-ku, Tokyo 164-8555, Japan;National Institute of Genetics. 1111 Yata, Mishima-city, Shizuoka 411-8540, Japan

  • Venue:
  • Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
  • Year:
  • 2003

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Abstract

This paper discusses the pattern matching problem for points under non-uniform distortions, which arises from the analysis of two-dimensional (2-D) electrophoresis images. First, we provide a formal definition of the problem. Next, we prove that it is NP-hard in two (or more) dimensions. This proof is based on a reduction from planar 3SAT. Then we present a simple polynomial time algorithm for a special and one-dimensional case of the problem, which is based on dynamic programming. We also present a practical heuristic algorithm for identifying a match between two sets of spots in 2-D gel electrophoresis images obtained from genomic DNA.