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Functional Similarity Analyzing of Protein Sequences with Empirical Mode Decomposition

This paper applies empirical mode decomposition (EMD) to find functional similarity of proteins with low identity. The cross-correlation coefficient based on the EMD is used to measure the pair-wise similarity. We also use a segmentation technique, combined with EMD, to handle long protein sequences. The results are compared with those using the pair-wise alignment and PSI-BLAST.