Algorithm, applications and evaluation for protein comparison by Ramanujan Fourier transform.
The amino acid sequence of a protein determines its chemical properties, chain conformation and biological functions. Protein sequence comparison is of great importance to identify similarities of protein structures and infer their functions. Many properties of a protein correspond to the low-frequency signals within the sequence. Low frequency modes in protein sequences are linked to the secondary structures, membrane protein types, and sub-cellular localizations of the proteins. In this paper, we present Ramanujan Fourier transform (RFT) with a fast algorithm to analyze the low-frequency signals of protein sequences. The RFT method is applied to similarity analysis of protein sequences with the Resonant Recognition Model (RRM). The results show that the proposed fast RFT method on protein comparison is more efficient than commonly used discrete Fourier transform (DFT). RFT can detect common frequencies as significant feature for specific protein families, and the RFT spectrum heat-map of protein sequences demonstrates the information conservation in the sequence comparison. The proposed method offers a new tool for pattern recognition, feature extraction and structural analysis on protein sequences.
School of Science, Nanjing Tech University, Nanjing, 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China. Electronic address: zhaojian@njtech.edu.cn.
Jian
J
Zhao
Department of Mathematics, Nanjing University, Nanjing, 210093, China.
Jiasong
J
Wang
Department of Basic Courses, Nanjing Institute of Technology, Nanjing, 211167, China.
Wei
W
Hua
College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
Pingkai
P
Ouyang
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005583:Fourier Analysis; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D011506:Proteins
Protein sequences comparison; Ramanujan Fourier (RT); Ramanujan Fourier transform (RFT); Resonant Recognition Model (RRM); Signal-to-noise ratio (SNR)