Functional comparisons of proteins using the wavelet packet transform

Some of structures and functions of a protein can be known from the information contained in its amino acid sequence. Proteins with similar amino acid sequences normally have close functions. Therefore, the similarity of proteins is one of the important research areas in protein analysis. To find the similarities of proteins, a hierarchical comparison method is used in this work. It is based on wavelet packet transform (WPT). The protein sequences are analyzed at their different components. The similarity of two proteins is obtained by using a cross-correlation formula. The results show that the wavelet packet transform can be used to detect the functional relationship via a similarity vector. This similarity approach is a kind of expansion of sequence similarity methods, which mainly focus on the alignment of amino acids.