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

• Main Authors: He Junjian, Wei Guifang, Zhang Yulei, Kou Chunhai, Xu Kexue, Wang Lianjie, Cao Youfang, Wang Yunfang, Zhao Liping
• Format: Article
• Language: English
• Published: BMC 2005-07-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/6/190
• ISSN: 1471-2105

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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 <it>in silico </it>PCR and gene finding.</p>