{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T06:36:44Z","timestamp":1757313404851},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats: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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats: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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats: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 <jats:italic>in silico<\/jats:italic> PCR and gene finding.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-190","type":"journal-article","created":{"date-parts":[[2005,7,28]],"date-time":"2005-07-28T00:06:44Z","timestamp":1122509204000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates"],"prefix":"10.1186","volume":"6","author":[{"given":"Youfang","family":"Cao","sequence":"first","affiliation":[]},{"given":"Lianjie","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Kexue","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Chunhai","family":"Kou","sequence":"additional","affiliation":[]},{"given":"Yulei","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Guifang","family":"Wei","sequence":"additional","affiliation":[]},{"given":"Junjian","family":"He","sequence":"additional","affiliation":[]},{"given":"Yunfang","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Liping","family":"Zhao","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,7,26]]},"reference":[{"issue":"11","key":"515_CR1","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1016\/0968-0004(93)90148-G","volume":"18","author":"WR Engels","year":"1993","unstructured":"Engels WR: Contributing software to the internet: the Amplify program. Trends Biochem Sci 1993, 18(11):448\u2013450. 10.1016\/0968-0004(93)90148-G","journal-title":"Trends Biochem Sci"},{"issue":"18","key":"515_CR2","doi-asserted-by":"publisher","first-page":"3538","DOI":"10.1093\/nar\/24.18.3538","volume":"24","author":"E Rubin","year":"1996","unstructured":"Rubin E, Levy AA: A mathematical model and a computerized simulation of PCR using complex templates. Nucleic Acids Res 1996, 24(18):3538\u20133545. 10.1093\/nar\/24.18.3538","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"515_CR3","doi-asserted-by":"publisher","first-page":"1879","DOI":"10.1093\/nar\/28.9.1879","volume":"28","author":"K Nishigaki","year":"2000","unstructured":"Nishigaki K, Saito A, Takashi H, Naimuddin M: Whole genome sequence-enabled prediction of sequences performed for random PCR products of Escherichia coli. Nucleic Acids Res 2000, 28(9):1879\u20131884. 10.1093\/nar\/28.9.1879","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"515_CR4","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1093\/bioinformatics\/17.2.192","volume":"17","author":"M Lexa","year":"2001","unstructured":"Lexa M, Horak J, Brzobohaty B: Virtual PCR. Bioinformatics 2001, 17(2):192\u2013193. 10.1093\/bioinformatics\/17.2.192","journal-title":"Bioinformatics"},{"issue":"15","key":"515_CR5","doi-asserted-by":"publisher","first-page":"2399","DOI":"10.1093\/bioinformatics\/bth257","volume":"20","author":"PC Boutros","year":"2004","unstructured":"Boutros PC, Okey AB: PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinformatics 2004, 20(15):2399\u20132400. 10.1093\/bioinformatics\/bth257","journal-title":"Bioinformatics"},{"key":"515_CR6","first-page":"208","volume-title":"Algorithms for Probe Selection and DNA Microarray Design","author":"S Rahmann","year":"2004","unstructured":"Rahmann S: Algorithms for Probe Selection and DNA Microarray Design. Volume Doctorate. Berlin , Free University of Berlin; 2004:208."},{"issue":"11","key":"515_CR7","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1093\/bioinformatics\/17.11.1067","volume":"17","author":"F Li","year":"2001","unstructured":"Li F, Stormo GD: Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 2001, 17(11):1067\u20131076. 10.1093\/bioinformatics\/17.11.1067","journal-title":"Bioinformatics"},{"issue":"10","key":"515_CR8","doi-asserted-by":"publisher","first-page":"1340","DOI":"10.1093\/bioinformatics\/18.10.1340","volume":"18","author":"L Kaderali","year":"2002","unstructured":"Kaderali L, Schliep A: Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 2002, 18(10):1340\u20131349. 10.1093\/bioinformatics\/18.10.1340","journal-title":"Bioinformatics"},{"issue":"18","key":"515_CR9","doi-asserted-by":"publisher","first-page":"2486","DOI":"10.1093\/bioinformatics\/btg350","volume":"19","author":"M Lexa","year":"2003","unstructured":"Lexa M, Valle G: PRIMEX: rapid identification of oligonucleotide matches in whole genomes. Bioinformatics 2003, 19(18):2486\u20132488. 10.1093\/bioinformatics\/btg350","journal-title":"Bioinformatics"},{"issue":"1","key":"515_CR10","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1471-2105-4-19","volume":"4","author":"HJ Purohit","year":"2003","unstructured":"Purohit HJ, Raje DV, Kapley A: Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. BMC Bioinformatics 2003, 4(1):19. 10.1186\/1471-2105-4-19","journal-title":"BMC Bioinformatics"},{"issue":"1-2","key":"515_CR11","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1574-6968.1995.tb07454.x","volume":"127","author":"A Grifoni","year":"1995","unstructured":"Grifoni A, Bazzicalupo M, Di Serio C, Fancelli S, Fani R: Identification of Azospirillum strains by restriction fragment length polymorphism of the 16S rDNA and of the histidine operon. FEMS Microbiol Lett 1995, 127(1\u20132):85\u201391. 10.1016\/0378-1097(95)00042-4","journal-title":"FEMS Microbiol Lett"},{"issue":"3","key":"515_CR12","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/S0014-5793(98)01294-0","volume":"438","author":"F Cremazy","year":"1998","unstructured":"Cremazy F, Soullier S, Berta P, Jay P: Further complexity of the human SOX gene family revealed by the combined use of highly degenerate primers and nested PCR. FEBS Lett 1998, 438(3):311\u2013314. 10.1016\/S0014-5793(98)01294-0","journal-title":"FEBS Lett"},{"issue":"17","key":"515_CR13","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"515_CR14","doi-asserted-by":"publisher","first-page":"1953","DOI":"10.1056\/NEJMoa030781","volume":"348","author":"TG Ksiazek","year":"2003","unstructured":"Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ: A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 2003, 348(20):1953\u20131966. 10.1056\/NEJMoa030781","journal-title":"N Engl J Med"},{"issue":"2","key":"515_CR15","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/S0168-1702(99)00017-9","volume":"60","author":"CB Stephensen","year":"1999","unstructured":"Stephensen CB, Casebolt DB, Gangopadhyay NN: Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay. Virus Res 1999, 60(2):181\u2013189. 10.1016\/S0168-1702(99)00017-9","journal-title":"Virus Res"},{"issue":"3","key":"515_CR16","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1016\/S0006-3495(97)78756-3","volume":"72","author":"MK Gilson","year":"1997","unstructured":"Gilson MK, Given JA, Bush BL, McCammon JA: The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997, 72(3):1047\u20131069.","journal-title":"Biophys J"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-190.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:44:53Z","timestamp":1706809493000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-190"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,7,26]]},"references-count":16,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["515"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-190","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,7,26]]},"assertion":[{"value":"18 March 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 July 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 July 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"190"}}