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We developed a new method to search protein networks functionally similar to a given query signal transduction pathway within protein interaction networks. This method consists of two parts: 1) a backtracking search algorithm to find topologically identical subgraphs and 2) a measurement of similarity between proteins by using Gene Ontology . For validation of our method, we implemented a software tool and compared its performance with that of PathBLAST  on the search of MAPK signal transduction cascades . The result showed that our software tool has equal or better performance than that of PathBLAST.