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So as to construct the new tool to classify the ubiquitin amino acid residues, we employed the random forest model to classify the ubiquitin sites utilizing the experimentally identified ubiquitinated protein sequences of A. thaliana. More detailed, we utilized the k-spaced amino acid pair (CKSAAP) encoding and binary encoding to deal with the potential protein segments. The proposed tools can obtain 72.83% in Sp, 72.42% in Sn, 72.63% in Acc, and 0.4525 in MCC. 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