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


CONCLUSIONS
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.
Cao
Youfang
Y
School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. yfcao@sjtu.edu.cn
Wang
Lianjie
L
Xu
Kexue
K
Kou
Chunhai
C
Zhang
Yulei
Y
Wei
Guifang
G
He
Junjian
J
Wang
Yunfang
Y
Zhao
Liping
L
D000465:Algorithms; D017124:Conserved Sequence; D020459:Genes, rRNA / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D016247:Information Storage and Retrieval / Q000379:methods; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D013698:Templates, Genetic