Analyzing functional similarity of protein sequences with discrete wavelet transform

Computational biology and Chemistry,2005, 29, 220-228

Qing XIONG  , Zhining Wen  , Ke Long Wang  , Menglong Li*  , Fu Sheng NIE 


This paper applies discrete wavelet transform (DWT) with various protein substitution models to find functional similarity of proteins with low identity. A new metric, ‘S’ function, based on the DWT is proposed to measure the pair-wise similarity. We also develop a segmentation technique, combined with DWT, to handle long protein sequences. The results are compared with those using the pair-wise alignment and PSI-BLAST.

Computational biology and Chemistry