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Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

Youfang Cao1, Lianjie Wang2, Kexue Xu4, Chunhai Kou3, Yulei Zhang1, Guifang Wei1, Junjian He1, Yunfang Wang1 and Liping Zhao1*

Author Affiliations

1 School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China

2 Department of Food Science and Engineering, Northwest Institute of Light Industry, Xianyang 712081, Shaanxi, China

3 Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China

4 Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China

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BMC Bioinformatics 2005, 6:190  doi:10.1186/1471-2105-6-190

Published: 26 July 2005



A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process.


Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template.


Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding.