{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,2]],"date-time":"2025-07-02T19:09:31Z","timestamp":1751483371452},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,9,8]],"date-time":"2009-09-08T00:00:00Z","timestamp":1252368000000},"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":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-281","type":"journal-article","created":{"date-parts":[[2009,9,8]],"date-time":"2009-09-08T02:15:36Z","timestamp":1252376136000},"source":"Crossref","is-referenced-by-count":17,"title":["Context-driven discovery of gene cassettes in mobile integrons using a computational grammar"],"prefix":"10.1186","volume":"10","author":[{"given":"Guy","family":"Tsafnat","sequence":"first","affiliation":[]},{"given":"Enrico","family":"Coiera","sequence":"additional","affiliation":[]},{"given":"Sally R","family":"Partridge","sequence":"additional","affiliation":[]},{"given":"Jaron","family":"Schaeffer","sequence":"additional","affiliation":[]},{"given":"Jon R","family":"Iredell","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,9,8]]},"reference":[{"issue":"23","key":"3011_CR1","doi-asserted-by":"publisher","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","volume":"27","author":"AL Delcher","year":"1999","unstructured":"Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27(23):4636\u20134641. 10.1093\/nar\/27.23.4636","journal-title":"Nucleic Acids Res"},{"key":"3011_CR2","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1093\/bioinformatics\/17.1.44","volume":"17","author":"D Frishman","year":"2001","unstructured":"Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, Zollner A, Mewes HW: Functional and structural genomics using PEDANT. Bioinformatics 2001, 17: 44\u201357. 10.1093\/bioinformatics\/17.1.44","journal-title":"Bioinformatics"},{"issue":"8","key":"3011_CR3","doi-asserted-by":"publisher","first-page":"3431","DOI":"10.1021\/cr068308h","volume":"107","author":"R Overbeek","year":"2007","unstructured":"Overbeek R, Bartels D, Vonstein V, Meyer F: Annotation of bacterial and archaeal genomes: improving accuracy and consistency. Chem Rev 2007, 107(8):3431\u20133447. 10.1021\/cr068308h","journal-title":"Chem Rev"},{"issue":"7","key":"3011_CR4","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/35080529","volume":"2","author":"L Stein","year":"2001","unstructured":"Stein L: Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2(7):493\u2013503. 10.1038\/35080529","journal-title":"Nat Rev Genet"},{"key":"3011_CR5","doi-asserted-by":"crossref","unstructured":"van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo AC, Dong X, Lu P, Szafron D, Greiner R, Wishart DS: BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 2005, (33 Web Server):W455-W459. 10.1093\/nar\/gki593","DOI":"10.1093\/nar\/gki593"},{"issue":"8","key":"3011_CR6","doi-asserted-by":"publisher","first-page":"2187","DOI":"10.1093\/nar\/gkg312","volume":"31","author":"F Meyer","year":"2003","unstructured":"Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, P\u00fchler A: GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003, 31(8):2187\u20132195. 10.1093\/nar\/gkg312","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"3011_CR7","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1371\/journal.pcbi.0010022","volume":"1","author":"H Quesneville","year":"2005","unstructured":"Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D: Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 2005, 1(2):166\u2013175. 10.1371\/journal.pcbi.0010022","journal-title":"PLoS Comput Biol"},{"issue":"10","key":"3011_CR8","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","volume":"16","author":"K Rutherford","year":"2000","unstructured":"Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B: Artemis: sequence visualization and annotation. Bioinformatics 2000, 16(10):944\u2013945. 10.1093\/bioinformatics\/16.10.944","journal-title":"Bioinformatics"},{"issue":"5","key":"3011_CR9","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1093\/bioinformatics\/15.5.391","volume":"15","author":"MA Andrade","year":"1999","unstructured":"Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C: Automated genome sequence analysis and annotation. Bioinformatics 1999, 15(5):391\u2013412. 10.1093\/bioinformatics\/15.5.391","journal-title":"Bioinformatics"},{"key":"3011_CR10","doi-asserted-by":"crossref","unstructured":"Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2007, (35 Database):D21-D25. 10.1093\/nar\/gkl986","DOI":"10.1093\/nar\/gkl986"},{"key":"3011_CR11","doi-asserted-by":"crossref","unstructured":"Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006, (34 Database):D187-D191. 10.1093\/nar\/gkj161","DOI":"10.1093\/nar\/gkj161"},{"key":"3011_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25\u20139. 10.1038\/75556","journal-title":"Nat Genet"},{"issue":"6","key":"3011_CR13","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/nrmicro909","volume":"2","author":"F Baquero","year":"2004","unstructured":"Baquero F: From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2004, 2(6):510\u2013518. 10.1038\/nrmicro909","journal-title":"Nat Rev Microbiol"},{"issue":"12","key":"3011_CR14","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1111\/j.1365-2958.1989.tb00153.x","volume":"3","author":"HW Stokes","year":"1989","unstructured":"Stokes HW, Hall RM: A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 1989, 3(12):1669\u20131683. 10.1111\/j.1365-2958.1989.tb00153.x","journal-title":"Mol Microbiol"},{"key":"3011_CR15","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1111\/j.1749-6632.1999.tb08916.x","volume":"870","author":"S Ji","year":"1999","unstructured":"Ji S: The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics. Annals of the New York Academy of Sciences 1999, 870: 411. 10.1111\/j.1749-6632.1999.tb08916.x","journal-title":"Annals of the New York Academy of Sciences"},{"issue":"6912","key":"3011_CR16","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nature01255","volume":"420","author":"DB Searls","year":"2002","unstructured":"Searls DB: The language of genes. Nature 2002, 420(6912):211\u2013217. 10.1038\/nature01255","journal-title":"Nature"},{"issue":"3","key":"3011_CR17","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1093\/bioinformatics\/17.3.226","volume":"17","author":"S Leung","year":"2001","unstructured":"Leung S, Mellish C, Robertson D: Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences. Bioinformatics 2001, 17(3):226\u2013236. 10.1093\/bioinformatics\/17.3.226","journal-title":"Bioinformatics"},{"issue":"4","key":"3011_CR18","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1093\/bioinformatics\/16.4.334","volume":"16","author":"E Rivas","year":"2000","unstructured":"Rivas E, Eddy SR: The language of RNA: a formal grammar that includes pseudoknots. Bioinformatics 2000, 16(4):334\u2013340. 10.1093\/bioinformatics\/16.4.334","journal-title":"Bioinformatics"},{"issue":"2","key":"3011_CR19","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S1368-7646(98)80026-5","volume":"1","author":"RM Hall","year":"1998","unstructured":"Hall RM, Collis CM: Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons. Drug Resist Updat 1998, 1(2):109\u2013119. 10.1016\/S1368-7646(98)80026-5","journal-title":"Drug Resist Updat"},{"issue":"4","key":"3011_CR20","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1111\/j.1574-6976.2009.00175.x","volume":"33","author":"SR Partridge","year":"2009","unstructured":"Partridge SR, Tsafnat G, Coiera E, Iredell JR: Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 2009, 33(4):757\u2013784. 10.1111\/j.1574-6976.2009.00175.x","journal-title":"FEMS Microbiol Rev"},{"key":"3011_CR21","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1186\/1471-2105-9-386","volume":"9","author":"F Meyer","year":"2008","unstructured":"Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9: 386. 10.1186\/1471-2105-9-386","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"3011_CR22","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","volume":"23","author":"AL Delcher","year":"2007","unstructured":"Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosym-biont DNA with Glimmer. Bioinformatics 2007, 23(6):673\u2013679. 10.1093\/bioinformatics\/btm009","journal-title":"Bioinformatics"},{"key":"3011_CR23","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28: 27\u201330. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"3011_CR24","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1093\/bioinformatics\/btp105","volume":"25","author":"A Moura","year":"2009","unstructured":"Moura A, Soares M, Pereira C, ao NL, Henriques I, Correia A: INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 2009, 25(8):1096\u20131098. 10.1093\/bioinformatics\/btp105","journal-title":"Bioinformatics"},{"key":"3011_CR25","doi-asserted-by":"crossref","unstructured":"Liu B, Pop M: ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, (37 Database):D443-D447. 10.1093\/nar\/gkn656","DOI":"10.1093\/nar\/gkn656"},{"key":"3011_CR26","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1186\/1471-2105-10-118","volume":"10","author":"MJ Joss","year":"2009","unstructured":"Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y: ACID: annotation of cassette and integron data. BMC Bioinformatics 2009, 10: 118. 10.1186\/1471-2105-10-118","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"3011_CR27","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1101\/gr.617103","volume":"13","author":"DA Rowe-Magnus","year":"2003","unstructured":"Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D: Comparative analysis of super-integrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res 2003, 13(3):428\u2013442. 10.1101\/gr.617103","journal-title":"Genome Res"},{"issue":"3","key":"3011_CR28","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410.","journal-title":"J Mol Biol"},{"issue":"8","key":"3011_CR29","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"WR Pearson","year":"1988","unstructured":"Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85(8):2444\u20132448. 10.1073\/pnas.85.8.2444","journal-title":"Proc Natl Acad Sci USA"},{"key":"3011_CR30","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2148-6-3","volume":"6","author":"Y Boucher","year":"2006","unstructured":"Boucher Y, Nesbo CL, Joss MJ, Robinson A, Mabbutt BC, Gillings MR, Doolittle WF, Stokes HW: Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. BMC Evol Biol 2006, 6: 3. 10.1186\/1471-2148-6-3","journal-title":"BMC Evol Biol"},{"issue":"7","key":"3011_CR31","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"ACE Darling","year":"2004","unstructured":"Darling ACE, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394\u20131403. 10.1101\/gr.2289704","journal-title":"Genome Res"},{"key":"3011_CR32","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1186\/1471-2105-9-459","volume":"9","author":"U Bohnebeck","year":"2008","unstructured":"Bohnebeck U, Lombardot T, Kottmann R, Gl\u00f6ckner FO: MetaMine-a tool to detect and analyse gene patterns in their environmental context. BMC Bioinformatics 2008, 9: 459. 10.1186\/1471-2105-9-459","journal-title":"BMC Bioinformatics"},{"key":"3011_CR33","doi-asserted-by":"crossref","unstructured":"Anderson T, Darling D: Asymptotic theory of certain goodness of fit criteria based on stochastic processes. Ann Math Statist 1952., 23(2): 10.1214\/aoms\/1177729437","DOI":"10.1214\/aoms\/1177729437"},{"issue":"4","key":"3011_CR34","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1128\/AAC.37.4.761","volume":"37","author":"IT Paulsen","year":"1993","unstructured":"Paulsen IT, Littlejohn TG, R\u00e5dstr\u00f6m P, Sundstrm L, Sk\u00f6ld O, Swedberg G, Skurray RA: The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants. Antimicrob Agents Chemother 1993, 37(4):761\u2013768.","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"3011_CR35","doi-asserted-by":"publisher","first-page":"2863","DOI":"10.1128\/AAC.00449-06","volume":"50","author":"RS Levings","year":"2006","unstructured":"Levings RS, Lightfoot D, Elbourne LDH, Djordjevic SP, Hall RM: New integron-associated gene cassette encoding a trimethoprim-resistant DfrB-type dihydrofolate reductase. Antimicrob Agents Chemother 2006, 50(8):2863\u20132865. 10.1128\/AAC.00449-06","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"3011_CR36","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1037\/h0031619","volume":"76","author":"J Fleiss","year":"1971","unstructured":"Fleiss J: Measuring nominal scale agreement among many raters. Psychological Bulletin 1971, 76(5):378\u2013382. 10.1037\/h0031619","journal-title":"Psychological Bulletin"},{"key":"3011_CR37","doi-asserted-by":"publisher","first-page":"159","DOI":"10.2307\/2529310","volume":"33","author":"J Landis","year":"1977","unstructured":"Landis J, Koch G: The measurement of observer agreement for categorical data. Biometrics 1977, 33: 159\u2013174. 10.2307\/2529310","journal-title":"Biometrics"},{"key":"3011_CR38","volume-title":"Information Retrieval","author":"CJ van Rijsbergen","year":"1979","unstructured":"van Rijsbergen CJ: Information Retrieval. Butterworth-Heinemann Newton, MA, USA; 1979."},{"key":"3011_CR39","doi-asserted-by":"crossref","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13-D21.","DOI":"10.1093\/nar\/gkm1000"},{"issue":"4","key":"3011_CR40","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1046\/j.1365-2958.1997.6091980.x","volume":"26","author":"HW Stokes","year":"1997","unstructured":"Stokes HW, O'Gorman DB, Recchia GD, Parsekhian M, Hall RM: Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol 1997, 26(4):731\u2013745. 10.1046\/j.1365-2958.1997.6091980.x","journal-title":"Mol Microbiol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-281.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-281\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-281.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T08:20:07Z","timestamp":1558513207000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-281"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,9,8]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3011"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-281","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,9,8]]},"article-number":"281"}}