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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2005-12

AUTHORS

Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, Yulei Zhang, Guifang Wei, Junjian He, Yunfang Wang, Liping Zhao

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. More... »

PAGES

190

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-6-190

DOI

http://dx.doi.org/10.1186/1471-2105-6-190

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1038016276

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16042814


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