Abstract
The structure of DNA binding proteins is identified that has great significance for the study of gene expression regulation mechanism.The new recognition method is proposed to identify the super-secondary structure and structure domain of DNA-binding protein in this paper. The nucleotide transition probability is calculated by the known DNA-binding protein binding locus sequence. Using mouse data which downloaded from the TRANSFAC establish the binding protein super-secondary structure recognition models. The probability score is calculated by the transition probability of the binding site and the background. This method differs from the conventional method, It is neither the amino acid sequence of the protein, nor the use of homologous proteins. In order to verify the validity of the algorithm, 10 DNA-binding proteins of drosophila and yeast are used to do the experiment. The experimental results show that our method has very good recognition result.
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