Author: Jia, Cangzhi; Liu, Tian; Zhang, Xiangde; Fu, Haoyue; Yang, Qing
Title: Alignment-free comparison of protein sequences based on reduced amino acid alphabets. Cord-id: vfhyi37f Document date: 2009_1_1
ID: vfhyi37f
Snippet: Protein sequences are treated as stochastic processes on the basis of a reduced amino acid alphabet of 10 types of amino acids. The realization of a stochastic process is described by associated transition probability matrix that corresponds to the process uniquely. Then new distances between transition probability matrices are defined for sequences similarity analysis. Two separate datasets are prepared and tested to identify the validity of the method. The results demonstrate the new method is
Document: Protein sequences are treated as stochastic processes on the basis of a reduced amino acid alphabet of 10 types of amino acids. The realization of a stochastic process is described by associated transition probability matrix that corresponds to the process uniquely. Then new distances between transition probability matrices are defined for sequences similarity analysis. Two separate datasets are prepared and tested to identify the validity of the method. The results demonstrate the new method is powerful and efficient.
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