{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T19:45:55Z","timestamp":1767383155320},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,2,21]],"date-time":"2007-02-21T00:00:00Z","timestamp":1172016000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-58","type":"journal-article","created":{"date-parts":[[2007,2,21]],"date-time":"2007-02-21T19:26:22Z","timestamp":1172085982000},"source":"Crossref","is-referenced-by-count":4,"title":["Sequence similarity is more relevant than species specificity in probabilistic backtranslation"],"prefix":"10.1186","volume":"8","author":[{"given":"Alfredo","family":"Ferro","sequence":"first","affiliation":[]},{"given":"Rosalba","family":"Giugno","sequence":"additional","affiliation":[]},{"given":"Giuseppe","family":"Pigola","sequence":"additional","affiliation":[]},{"given":"Alfredo","family":"Pulvirenti","sequence":"additional","affiliation":[]},{"given":"Cinzia","family":"Di Pietro","sequence":"additional","affiliation":[]},{"given":"Michele","family":"Purrello","sequence":"additional","affiliation":[]},{"given":"Marco","family":"Ragusa","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,2,21]]},"reference":[{"key":"1430_CR1","unstructured":"Software SGD[\n                    http:\/\/www.evolvingcode.net\/codon\/\n                    \n                  ]"},{"key":"1430_CR2","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1101\/gr.4431306","volume":"16","author":"S Richardson","year":"2006","unstructured":"Richardson S, Wheelan S, Yarrington R, Boeke J: GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res 2006, 16: 550\u2013556. 10.1101\/gr.4431306","journal-title":"Genome Res"},{"key":"1430_CR3","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1186\/1471-2105-7-285","volume":"7","author":"A Villalobos","year":"2006","unstructured":"Villalobos A, Ness J, Gustafsson C, Minshull J, Govindarajan S: Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006, 7: 285. 10.1186\/1471-2105-7-285","journal-title":"BMC Bioinformatics"},{"key":"1430_CR4","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/1471-2105-6-182","volume":"6","author":"F Supek","year":"2005","unstructured":"Supek F, Vlahovi\u010dek K: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics 2005, 6: 182. 10.1186\/1471-2105-6-182","journal-title":"BMC Bioinformatics"},{"key":"1430_CR5","doi-asserted-by":"publisher","first-page":"r43","DOI":"10.1093\/nar\/9.1.213-b","volume":"9","author":"R Grantham","year":"1981","unstructured":"Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R: Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 1981, 9: r43-r74. 10.1093\/nar\/9.1.213-b","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1430_CR6","doi-asserted-by":"publisher","first-page":"r49","DOI":"10.1093\/nar\/8.1.197-c","volume":"8","author":"R Grantham","year":"1980","unstructured":"Grantham R, Gautier C, Gouy M, Mercier R, Pave A: Codon catalog usage and the genome hypothesis. Nucleic Acids Res 1980, 8(1):r49-r62. 10.1093\/nar\/8.1.197-c","journal-title":"Nucleic Acids Res"},{"key":"1430_CR7","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.biosystems.2003.10.001","volume":"73","author":"W Gu","year":"2004","unstructured":"Gu W, Zhou T, Ma J, Sun X, Lu Z: The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens . Biosystems 2004, 73: 89\u201397. 10.1016\/j.biosystems.2003.10.001","journal-title":"Biosystems"},{"key":"1430_CR8","doi-asserted-by":"publisher","first-page":"8207","DOI":"10.1093\/nar\/16.17.8207","volume":"16","author":"P Sharp","year":"1988","unstructured":"Sharp P, Cowe E, Higgins D: Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens : a review of the considerable within-species diversity. Nucleic Acids Res 1988, 16: 8207\u20138211. 10.1093\/nar\/16.17.8207","journal-title":"Nucleic Acids Res"},{"key":"1430_CR9","doi-asserted-by":"publisher","first-page":"5125","DOI":"10.1093\/nar\/14.13.5125","volume":"14","author":"P Sharp","year":"1986","unstructured":"Sharp P, Tuohy T, Mosurski K: Codon usage in yeast : cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 1986, 14: 5125\u20135143. 10.1093\/nar\/14.13.5125","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1430_CR10","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1093\/nar\/16.5.1715","volume":"15","author":"G Pesole","year":"1988","unstructured":"Pesole G, Attimonelli M, Liuni S: A backtranslation method based on codon usage strategy. Nucleic Acids Res 1988, 15(5):1715\u20131728. 10.1093\/nar\/16.5.1715","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1430_CR11","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the european molecular biology open software suite. Trends Genet 2000, 16(6):276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"},{"issue":"13","key":"1430_CR12","doi-asserted-by":"publisher","first-page":"2148","DOI":"10.1093\/bioinformatics\/bth204","volume":"20","author":"A Moreira","year":"2004","unstructured":"Moreira A, Maass A: TIP: protein backtranslation aided by genetic algorithms. Bioinformatics 2004, 20(13):2148\u20132149. 10.1093\/bioinformatics\/bth204","journal-title":"Bioinformatics"},{"issue":"2","key":"1430_CR13","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.tcs.2004.03.014","volume":"322","author":"A Moreira","year":"2004","unstructured":"Moreira A: Genetic algorithm for the imitation of genomic styles in protein backtranslation. Theoretical Computer Science 2004, 322(2):297\u2013312. 10.1016\/j.tcs.2004.03.014","journal-title":"Theoretical Computer Science"},{"key":"1430_CR14","first-page":"231","volume-title":"Proceeding of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology San Diego, CA","author":"R Giugno","year":"2004","unstructured":"Giugno R, Pulvirenti A, Ragusa M, Facciola L, Patelmo L, Pietro VD, Pietro CD, Purrello M, Ferro A: Locally sensitive backtranslation based on multiple sequence alignment. Proceeding of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology San Diego, CA 2004, 231\u2013237."},{"issue":"2","key":"1430_CR15","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1109\/5.18626","volume":"77","author":"L Rabiner","year":"1989","unstructured":"Rabiner L: A tutorial on Hidden Markov Models and selected applications in speech recognition. Proceedings of The IEEE 1989, 77(2):257\u2013286. 10.1109\/5.18626","journal-title":"Proceedings of The IEEE"},{"key":"1430_CR16","unstructured":"NCBI[\n                    http:\/\/www.ncbi.nlm.nih.gov\/\n                    \n                  ]"},{"key":"1430_CR17","unstructured":"JFreeChart[\n                    http:\/\/jfree.org\/jfreechart\/\n                    \n                  ]"},{"key":"1430_CR18","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological sequence analysis: probabalistic models of proteins and nucleic acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy S, Krogh A, Mitchison G: Biological sequence analysis: probabalistic models of proteins and nucleic acids. Cambridge: Cambridge University Press; 1998."},{"key":"1430_CR19","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1101\/gr.2821705","volume":"15","author":"CD Do","year":"2005","unstructured":"Do CD, Mahabhashyam MSP, Brudno M, Batzoglou S: ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15: 330\u2013340. 10.1101\/gr.2821705","journal-title":"Genome Res"},{"issue":"30","key":"1430_CR20","doi-asserted-by":"publisher","first-page":"11030","DOI":"10.1073\/pnas.0404206101","volume":"101","author":"M Nei","year":"2004","unstructured":"Nei M, Kumar S: Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004, 101(30):11030\u201311035. 10.1073\/pnas.0404206101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"1430_CR21","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1089\/dna.2005.24.111","volume":"24","author":"M Purrello","year":"2005","unstructured":"Purrello M, Pietro CD, Ragusa M, Pulvirenti A, Giugno R, Pietro VD, Emmanuele G, Travali S, Scalia M, Shasha D, Ferro A: In vitro and in silico cloning of Xenopus laevis SOD2 and its phylogenetic analysis. DNA and Cell Biol 2005, 24(2):111\u2013116. 10.1089\/dna.2005.24.111","journal-title":"DNA and Cell Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-58\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T09:11:05Z","timestamp":1548234665000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-58"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,2,21]]},"references-count":21,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1430"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-58","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,2,21]]},"article-number":"58"}}