Dataset Information

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

ABSTRACT: BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.

SUBMITTER: Cao Y

PROVIDER: S-EPMC1183192 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature

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

Cao Youfang Y Wang Lianjie L Xu Kexue K Kou Chunhai C Zhang Yulei Y Wei Guifang G He Junjian J Wang Yunfang Y Zhao Liping L

BMC bioinformatics 20050726

<h4>Background</h4>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.<h4>Results</h4>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 ...[more]

PMID: 16042814

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Dataset Information

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

Publications

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

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