{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:53:22Z","timestamp":1740135202020,"version":"3.37.3"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,5,8]],"date-time":"2012-05-08T00:00:00Z","timestamp":1336435200000},"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":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-83","type":"journal-article","created":{"date-parts":[[2012,5,8]],"date-time":"2012-05-08T16:27:20Z","timestamp":1336494440000},"source":"Crossref","is-referenced-by-count":11,"title":["Detecting long tandem duplications in genomic sequences"],"prefix":"10.1186","volume":"13","author":[{"given":"Eric","family":"Audemard","sequence":"first","affiliation":[]},{"given":"Thomas","family":"Schiex","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Faraut","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,5,8]]},"reference":[{"issue":"12","key":"5240_CR1","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1038\/nrg2482","volume":"9","author":"GC Conant","year":"2008","unstructured":"Conant GC, Wolfe KH: Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 2008, 9(12):938\u2013950. http:\/\/dx.doi.org\/10.1038\/nrg2482 10.1038\/nrg2482","journal-title":"Nat Rev Genet"},{"issue":"5","key":"5240_CR2","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/jhered\/esp047","volume":"100","author":"MW Hahn","year":"2009","unstructured":"Hahn MW: Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered 2009, 100(5):605\u2013617. http:\/\/dx.doi.org\/10.1093\/jhered\/esp047 10.1093\/jhered\/esp047","journal-title":"J Hered"},{"issue":"2","key":"5240_CR3","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nrg2689","volume":"11","author":"H Innan","year":"2010","unstructured":"Innan H, Kondrashov F: The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 2010, 11(2):97\u2013108. http:\/\/dx.doi.org\/10.1038\/nrg2689","journal-title":"Nat Rev Genet"},{"key":"5240_CR4","volume-title":"PLoS One","author":"JP Demuth","year":"2006","unstructured":"Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW: The evolution of mammalian gene families. PLoS One 2006., e85+: http:\/\/dx.doi.org\/10.1371\/journal.pone.0000085"},{"issue":"11","key":"5240_CR5","doi-asserted-by":"publisher","first-page":"e197","DOI":"10.1371\/journal.pgen.0030197","volume":"3","author":"MW Hahn","year":"2007","unstructured":"Hahn MW, Han MV, Han SG: Gene family evolution across 12 Drosophila genomes. PLoS Genet 2007, 3(11):e197. http:\/\/dx.doi.org\/10.1371\/journal.pgen.0030197 10.1371\/journal.pgen.0030197","journal-title":"PLoS Genet"},{"issue":"11","key":"5240_CR6","doi-asserted-by":"publisher","first-page":"1698","DOI":"10.1101\/gr.082016.108","volume":"18","author":"GH Perry","year":"2008","unstructured":"Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R: Copy number variation and evolution in humans and chimpanzees. Genome Res 2008, 18(11):1698\u20131710. http:\/\/dx.doi.org\/10.1101\/gr.082016.108 10.1101\/gr.082016.108","journal-title":"Genome Res"},{"issue":"7231","key":"5240_CR7","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1038\/nature07744","volume":"457","author":"T Marques-Bonet","year":"2009","unstructured":"Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, Cardone MF, Navarro A, Mardis ER, Wilson RK, Eichler EE: A burst of segmental duplications in the genome of the African great ape ancestor. Nature 2009, 457(7231):877\u2013881. http:\/\/dx.doi.org\/10.1038\/nature07744 10.1038\/nature07744","journal-title":"Nature"},{"key":"5240_CR8","first-page":"2007","volume":"2007","author":"L Dumas","year":"2007","unstructured":"Dumas L, Kim YHH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JRR, Sikela JMM: Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 2007, 2007: 2007\u20132007. http:\/\/dx.doi.org\/10.1101\/gr.6557307","journal-title":"Genome Res"},{"issue":"1698","key":"5240_CR9","doi-asserted-by":"publisher","first-page":"3213","DOI":"10.1098\/rspb.2010.1180","volume":"277","author":"DR Schrider","year":"2010","unstructured":"Schrider DR, Hahn MW: Gene copy-number polymorphism in nature. Proc Biol Sci 2010, 277(1698):3213\u20133221. http:\/\/dx.doi.org\/10.1098\/rspb.2010.1180 10.1098\/rspb.2010.1180","journal-title":"Proc Biol Sci"},{"issue":"9","key":"5240_CR10","doi-asserted-by":"publisher","first-page":"e115","DOI":"10.1371\/journal.pcbi.0020115","volume":"2","author":"C Rizzon","year":"2006","unstructured":"Rizzon C, Ponger L, Gaut BS: Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2006, 2(9):e115. http:\/\/dx.doi.org\/10.1371\/journal.pcbi.0020115 10.1371\/journal.pcbi.0020115","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"5240_CR11","doi-asserted-by":"publisher","first-page":"2134","DOI":"10.1093\/molbev\/msl085","volume":"23","author":"V Shoja","year":"2006","unstructured":"Shoja V, Zhang L: A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. Mol Biol Evol 2006, 23(11):2134\u20132141. http:\/\/dx.doi.org\/10.1093\/molbev\/msl085 10.1093\/molbev\/msl085","journal-title":"Mol Biol Evol"},{"issue":"4","key":"5240_CR12","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1093\/genetics\/165.4.1793","volume":"165","author":"V Katju","year":"2003","unstructured":"Katju V, Lynch M: The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics 2003, 165(4):1793\u20131803.","journal-title":"Genetics"},{"issue":"13","key":"5240_CR13","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1093\/hmg\/11.13.1561","volume":"11","author":"I Letunic","year":"2002","unstructured":"Letunic I, Copley RR, Bork P: Common exon duplication in animals and its role in alternative splicing. Hum Mol Genet 2002, 11(13):1561\u20131567. 10.1093\/hmg\/11.13.1561","journal-title":"Hum Mol Genet"},{"issue":"5","key":"5240_CR14","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1101\/gr.6146507","volume":"17","author":"R Zhang","year":"2007","unstructured":"Zhang R, Peng Y, Wang W, Su B: Rapid evolution of an X-linked microRNA cluster in primates. Genome Res 2007, 17(5):612\u2013617. http:\/\/dx.doi.org\/10.1101\/gr.6146507 10.1101\/gr.6146507","journal-title":"Genome Res"},{"issue":"5494","key":"5240_CR15","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","volume":"290","author":"M Lynch","year":"2000","unstructured":"Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 2000, 290(5494):1151\u20131155. http:\/\/dx.doi.org\/10.1126\/science.290.5494.1151 10.1126\/science.290.5494.1151","journal-title":"Science"},{"key":"5240_CR16","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1023\/A:1022644628861","volume":"3","author":"WH Li","year":"2003","unstructured":"Li WH, Gu Z, Cavalcanti AR, Nekrutenko A: Detection of gene duplications and block duplications in eukaryotic genomes. J Struct Funct Genomics 2003, 3: 27\u201334. http:\/\/view.ncbi.nlm.nih.gov\/pubmed\/12836682 10.1023\/A:1022644628861","journal-title":"J Struct Funct Genomics"},{"key":"5240_CR17","volume-title":"The Origins of Genome Architecture","author":"M Lynch","year":"2007","unstructured":"Lynch M: The Origins of Genome Architecture. W.H. Freeman & Company; 2007. http:\/\/www.amazon.com\/exec\/obidos\/redirect?tag=citeulike07\u201320&path=ASIN\/0878934847"},{"issue":"2","key":"5240_CR18","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucl Acids Res 1999, 27(2):573\u2013580. http:\/\/dx.doi.org\/10.1093\/nar\/27.2.573 10.1093\/nar\/27.2.573","journal-title":"Nucl Acids Res"},{"issue":"13","key":"5240_CR19","doi-asserted-by":"publisher","first-page":"3672","DOI":"10.1093\/nar\/gkg617","volume":"31","author":"R Kolpakov","year":"2003","unstructured":"Kolpakov R, Bana G, Kucherov G: mreps: efficient and flexible detection of tandem repeats in DNA. Nucl Acids Res 2003, 31(13):3672\u20133678. http:\/\/dx.doi.org\/10.1093\/nar\/gkg617 10.1093\/nar\/gkg617","journal-title":"Nucl Acids Res"},{"key":"5240_CR20","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/1471-2164-11-56","volume":"11","author":"L Despons","year":"2010","unstructured":"Despons L, Baret PV, Frangeul L, Louis VL, Durrens P, Souciet JL: Genome-wide computational prediction of tandem gene arrays: application in yeasts. BMC Genomics 2010, 11: 56. http:\/\/dx.doi.org\/10.1186\/1471\u20132164\u201311\u201356 10.1186\/1471-2164-11-56","journal-title":"BMC Genomics"},{"issue":"6","key":"5240_CR21","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1101\/gr.GR-1871R","volume":"11","author":"JA Bailey","year":"2001","unstructured":"Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE: Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 2001, 11(6):1005\u20131017. http:\/\/dx.doi.org\/10.1101\/gr.187101 10.1101\/gr.GR-1871R","journal-title":"Genome Res"},{"issue":"10","key":"5240_CR22","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/j.tig.2009.08.002","volume":"25","author":"T Marques-Bonet","year":"2009","unstructured":"Marques-Bonet T, Girirajan S, Eichler EE: The origins and impact of primate segmental duplications. Trends Genet 2009, 25(10):443\u2013454. http:\/\/dx.doi.org\/10.1016\/j.tig.2009.08.002 10.1016\/j.tig.2009.08.002","journal-title":"Trends Genet"},{"issue":"18","key":"5240_CR23","doi-asserted-by":"publisher","first-page":"3643","DOI":"10.1093\/bioinformatics\/bth397","volume":"20","author":"BJ Haas","year":"2004","unstructured":"Haas BJ, Delcher AL, Wortman JR, Salzberg SL: DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 2004, 20(18):3643\u20133646. http:\/\/view.ncbi.nlm.nih.gov\/pubmed\/15247098 10.1093\/bioinformatics\/bth397","journal-title":"Bioinformatics"},{"key":"5240_CR24","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1093\/bioinformatics\/btp070","volume":"25","author":"T Hachiya","year":"2009","unstructured":"Hachiya T, Osana Y, Popendorf K, Sakakibara Y: Accurate identification of orthologous segments among multiple genomes. Bioinformatics 2009, 25: 853\u2013860. 10.1093\/bioinformatics\/btp070","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"5240_CR25","doi-asserted-by":"publisher","first-page":"S312","DOI":"10.1093\/bioinformatics\/18.suppl_1.S312","volume":"18","author":"M Hohl","year":"2002","unstructured":"Hohl M, Kurtz S, Ohlebusch E: Efficient multiple genome alignment. Bioinformatics 2002, 18(Suppl 1):S312-S320. http:\/\/eutils.ncbi.nlm.nih.gov\/entrez\/eutils\/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=12169561 10.1093\/bioinformatics\/18.suppl_1.S312","journal-title":"Bioinformatics"},{"issue":"6","key":"5240_CR26","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1101\/gr.2179004","volume":"14","author":"C Simillion","year":"2004","unstructured":"Simillion C, Vandepoele K, Saeys Y, de Peer YV: Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res 2004, 14(6):1095\u20131106. http:\/\/dx.doi.org\/10.1101\/gr.2179004 10.1101\/gr.2179004","journal-title":"Genome Res"},{"issue":"3","key":"5240_CR27","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. http:\/\/dx.doi.org\/10.1016\/S0022\u20132836(05)80360\u20132","journal-title":"J Mol Biol"},{"issue":"7","key":"5240_CR28","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1105\/tpc.12.7.1093","volume":"12","author":"G Blanc","year":"2000","unstructured":"Blanc G, Barakat A, Guyot R, Cooke R, Delseny M: Extensive duplication and reshuffling in the Arabidopsis genome. The Plant Cell Online 2000, 12(7):1093.","journal-title":"The Plant Cell Online"},{"key":"5240_CR29","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2229-4-10","volume":"4","author":"S Cannon","year":"2004","unstructured":"Cannon S, Mitra A, Baumgarten A, Young N, May G: The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 2004, 4: 10. 10.1186\/1471-2229-4-10","journal-title":"BMC Plant Biol"},{"key":"5240_CR30","first-page":"1028","volume-title":"J Comput Biol","author":"A Morgulis","year":"2006","unstructured":"Morgulis A, Gertz EM, Sch\u00c3\u00a4ffer AA, Agarwala R: A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. J Comput Biol 2006, 1028\u20131040."},{"issue":"12","key":"5240_CR31","doi-asserted-by":"publisher","first-page":"2533","DOI":"10.1101\/gr.1318503","volume":"13","author":"L Zhang","year":"2003","unstructured":"Zhang L, Gaut BS: Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome? Genome Res 2003, 13(12):2533\u20132540. http:\/\/dx.doi.org\/10.1101\/gr.1318503 10.1101\/gr.1318503","journal-title":"Genome Res"},{"key":"5240_CR32","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1093\/oxfordjournals.molbev.a026236","volume":"17","author":"Z Yang","year":"2000","unstructured":"Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000, 17: 32\u201343. http:\/\/mbe.oxfordjournals.org\/cgi\/content\/abstract\/17\/1\/32 10.1093\/oxfordjournals.molbev.a026236","journal-title":"Mol Biol Evol"},{"key":"5240_CR33","first-page":"555","volume":"13","author":"Z Yang","year":"1997","unstructured":"Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997, 13: 555\u2013556.","journal-title":"CABIOS"},{"issue":"10","key":"5240_CR34","doi-asserted-by":"publisher","first-page":"1313","DOI":"10.1101\/gr.101386.109","volume":"20","author":"H Kaessmann","year":"2010","unstructured":"Kaessmann H: Origins, evolution, and phenotypic impact of new genes. Genome Res 2010, 20(10):1313. 10.1101\/gr.101386.109","journal-title":"Genome Res"},{"issue":"6814","key":"5240_CR35","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1038\/35048500","volume":"408","author":"A Theologis","year":"2000","unstructured":"Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Aken SV, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW: Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 2000, 408(6814):816\u2013820. http:\/\/dx.doi.org\/10.1038\/35048500 10.1038\/35048500","journal-title":"Nature"},{"issue":"5780","key":"5240_CR36","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1126\/science.1126316","volume":"312","author":"L Duret","year":"2006","unstructured":"Duret L, Chureau C, Samain S, Weissenbach J, Avner P: The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 2006, 312(5780):1653. 10.1126\/science.1126316","journal-title":"Science"},{"key":"5240_CR37","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1093\/gbe\/evq033","volume":"2","author":"S DeBolt","year":"2010","unstructured":"DeBolt S: Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol 2010, 2: 441. 10.1093\/gbe\/evq033","journal-title":"Genome Biol Evol"},{"issue":"7","key":"5240_CR38","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","volume":"30","author":"AJ Enright","year":"2002","unstructured":"Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucl Acids Res 2002, 30(7):1575\u20131584. http:\/\/dx.doi.org\/10.1093\/nar\/30.7.1575 10.1093\/nar\/30.7.1575","journal-title":"Nucl Acids Res"},{"key":"5240_CR39","volume-title":"Nucleic Acids Res","author":"L No\u00e9","year":"2005","unstructured":"No\u00e9 L, Kucherov G: YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Res 2005., 33: http:\/\/view.ncbi.nlm.nih.gov\/pubmed\/15980530(WebServerissue)"},{"key":"5240_CR40","volume-title":"Network Flows: Theory, Algorithms, and Applications","author":"RK Ahuja","year":"1993","unstructured":"Ahuja RK, Magnanti TL, Orlin JB:Network Flows: Theory, Algorithms, and Applications. Prentice Hall; 1993. [ http:\/\/www.amazon.com\/exec\/obidos\/redirect?tag=citeulike07\u201320&path=ASIN\/013617549X ]"},{"key":"5240_CR41","volume-title":"ORO Technical Report 15","author":"R Busacker","year":"1961","unstructured":"Busacker R, Gowen P: A procedure for determining minimal-cost network flow patterns. ORO Technical Report 15 1961."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-83.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-83\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-83.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,15]],"date-time":"2022-01-15T05:26:21Z","timestamp":1642224381000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-83"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,8]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5240"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-83","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2012,5,8]]},"article-number":"83"}}