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Background: Reversible protein phosphorylation is one of the most important post-translational modifications, which regulates almost all basic cellular processes.So far, thousands of phosphorylation sites have been discovered by large-scale phospho-proteomics studies but only 8% of them have annotation of catalytic kinases, thus how to identify kinases for observed phosphorylation sites correctly remains a challenge.Most of the existing tools for identifying kinase-substrate relationships used only local sequence information to construct predictive models and currently few studies concern about hierarchical structures of kinases.