Table 2 Distance Matrix for human kinases PAK series. Distance measures D between various human kinases. PAK series are closely similar kinases, while PLK1 is a distant relative in the kinome evolutionary tree [27]. Smaller SSS values correspond to strong similarity. GAP (Needleman-Wuntch [9] algorithm implemented in gcg package) scores are in percentage similarity. F = 8, S _z = 4, β = 0.502. It can be seen that the dynamic programming approach used in the SSS algorithm is a simple but effective approach to ascertain global similarity. A replica of the branch of the kinome tree can be generated using the matrix.

From: Detailed protein sequence alignment based on Spectral Similarity Score (SSS)