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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. [Copyright &y& Elsevier]