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Analyzing functional similarity of protein sequences with discrete wavelet transform |
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| Authors: | Wen Zhi-ning Wang Ke-long Li Meng-long Nie Fu-sheng Yang Yi |
| Institution: | College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China. |
| Abstract: | 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. |
| Keywords: | Discrete wavelet transform Protein sequence analysis Substitution model Functional similarity evaluation |
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