{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T03:06:53Z","timestamp":1771643213785,"version":"3.50.1"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"S9","license":[{"start":{"date-parts":[[2011,10,5]],"date-time":"2011-10-05T00:00:00Z","timestamp":1317772800000},"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":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-s9-s6","type":"journal-article","created":{"date-parts":[[2011,10,5]],"date-time":"2011-10-05T18:48:07Z","timestamp":1317840487000},"source":"Crossref","is-referenced-by-count":28,"title":["A method for computing an inventory of metazoan mitochondrial gene order rearrangements"],"prefix":"10.1186","volume":"12","author":[{"given":"Matthias","family":"Bernt","sequence":"first","affiliation":[]},{"given":"Martin","family":"Middendorf","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,10,5]]},"reference":[{"issue":"8","key":"4813_CR1","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/27.8.1767","volume":"27","author":"JL Boore","year":"1999","unstructured":"Boore JL: Animal mitochondrial genomes. Nucleic Acids Res 1999, 27(8):1767\u20131780. 10.1093\/nar\/27.8.1767","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"4813_CR2","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1016\/S0959-437X(98)80035-X","volume":"8","author":"JL Boore","year":"1998","unstructured":"Boore JL, Brown WM: Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 1998, 8(6):668\u2013674. 10.1016\/S0959-437X(98)80035-X","journal-title":"Curr Opin Genet Dev"},{"issue":"12","key":"4813_CR3","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1093\/oxfordjournals.molbev.a025903","volume":"15","author":"WC Black IV","year":"1998","unstructured":"Black IV WC, Roehrdanz RL: Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol Biol Evol 1998, 15(12):1772\u20131785.","journal-title":"Mol Biol Evol"},{"key":"4813_CR4","first-page":"85","volume-title":"RECOMB Comparative Genomics, Volume 3388 of LNCS","author":"I Mikl\u00f3s","year":"2005","unstructured":"Mikl\u00f3s I, Hein J: Genome Rearrangement in Mitochondria and Its Computational Biology. RECOMB Comparative Genomics, Volume 3388 of LNCS 2005, 85\u201396."},{"issue":"2","key":"4813_CR5","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/S1016-8478(23)07372-7","volume":"23","author":"HJ Woo","year":"2007","unstructured":"Woo HJ, Lee YS, Park SJ, Lim JT, Jang KH, Choi EH, Choi YG, Hwang UW: Complete Mitochondrial Genome of a Troglobite Millipede Antrokoreana gracilipes (Diplopoda, Juliformia, Julida), and Juliformian Phylogeny. Mol Cells 2007, 23(2):182\u2013191.","journal-title":"Mol Cells"},{"issue":"3","key":"4813_CR6","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1016\/j.ympev.2005.10.018","volume":"38","author":"T Akasaki","year":"2006","unstructured":"Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Hasegawa M, Okada N: Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol Phylogenet Evol 2006, 38(3):648\u2013658. 10.1016\/j.ympev.2005.10.018","journal-title":"Mol Phylogenet Evol"},{"key":"4813_CR7","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1007\/978-94-011-4309-7_13","volume-title":"Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, Volume 1 of Computational Biology Series","author":"JL Boore","year":"2000","unstructured":"Boore JL: The duplication\/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, Volume 1 of Computational Biology Series. Edited by: Sankoff D, Nadeau JH. Kluwer Academic Publishers; 2000:133\u2013147."},{"key":"4813_CR8","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.ympev.2007.07.017","volume":"45","author":"L Podsiadlowski","year":"2007","unstructured":"Podsiadlowski L, Kohlhagen H, Koch M: The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. Mol Phylogenet Evol 2007, 45: 251\u2013260. 10.1016\/j.ympev.2007.07.017","journal-title":"Mol Phylogenet Evol"},{"key":"4813_CR9","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1186\/1471-2164-8-386","volume":"8","author":"K Fahrein","year":"2007","unstructured":"Fahrein K, Talarico G, Braband A, Podsiadlowski L: The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida. BMC Genomics 2007, 8: 386. 10.1186\/1471-2164-8-386","journal-title":"BMC Genomics"},{"issue":"2","key":"4813_CR10","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1093\/oxfordjournals.molbev.a004068","volume":"19","author":"DV Lavrov","year":"2002","unstructured":"Lavrov DV, Boore JL, Brown WM: Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss. Mol Biol Evol 2002, 19(2):163\u2013169. 10.1093\/oxfordjournals.molbev.a004068","journal-title":"Mol Biol Evol"},{"key":"4813_CR11","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1287\/ijoc.15.1.93.15155","volume":"15","author":"A Caprara","year":"2003","unstructured":"Caprara A: The Reversal Median Problem. INFORMS J Comput 2003, 15: 93\u2013113. 10.1287\/ijoc.15.1.93.15155","journal-title":"INFORMS J Comput"},{"key":"4813_CR12","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1186\/1471-2105-10-120","volume":"10","author":"E Tannier","year":"2009","unstructured":"Tannier E, Zheng C, Sankoff D: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 2009, 10: 120. 10.1186\/1471-2105-10-120","journal-title":"BMC Bioinformatics"},{"key":"4813_CR13","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1186\/1471-2105-9-516","volume":"9","author":"M Bader","year":"2008","unstructured":"Bader M, Abouelhoda M, Ohlebusch E: A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions. BMC Bioinformatics 2008, 9: 516. 10.1186\/1471-2105-9-516","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"4813_CR14","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/PL00006542","volume":"49","author":"M Blanchette","year":"1999","unstructured":"Blanchette M, Kunisawa T, Sankoff D: Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny. J Mol Evol 1999, 49(2):193\u2013203. 10.1007\/PL00006542","journal-title":"J Mol Evol"},{"key":"4813_CR15","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1007\/3-540-48194-X_19","volume-title":"Combinatorial Pattern Matching, Volume 2089 of LNCS","author":"S Heber","year":"2001","unstructured":"Heber S, Stoye J: Finding all Common Intervals of k Permutations. Combinatorial Pattern Matching, Volume 2089 of LNCS 2001, 207\u2013218."},{"key":"4813_CR16","first-page":"4","volume":"4","author":"S B\u00e9rard","year":"2007","unstructured":"B\u00e9rard S, Bergeron A, Chauve C, Paul C: Perfect sorting by reversals is not always difficult. IEEE ACM T Comput Bi 2007, 4: 4\u201316.","journal-title":"IEEE ACM T Comput Bi"},{"issue":"3","key":"4813_CR17","first-page":"332","volume":"5","author":"M Bernt","year":"2008","unstructured":"Bernt M, Merkle D, Middendorf M: Solving the Preserving Reversal Median Problem. IEEE ACM T Comput Bi 2008, 5(3):332\u2013347.","journal-title":"IEEE ACM T Comput Bi"},{"issue":"10","key":"4813_CR18","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1089\/cmb.2006.13.1685","volume":"13","author":"L Parida","year":"2006","unstructured":"Parida L: Using PQ Structures for Genomic Rearrangement Phylogeny. Journal of Computational Biology 2006, 13(10):1685\u20131700. 10.1089\/cmb.2006.13.1685","journal-title":"Journal of Computational Biology"},{"issue":"21","key":"4813_CR19","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btm468","volume":"23","author":"M Bernt","year":"2007","unstructured":"Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, Schlegel M, Stadler PF, Middendorf M: CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 2007, 23(21):2957\u20132958. 10.1093\/bioinformatics\/btm468","journal-title":"Bioinformatics"},{"key":"4813_CR20","first-page":"143","volume-title":"RECOMB Comparative Genomics, Volume 5267 of LNBI","author":"M Bernt","year":"2008","unstructured":"Bernt M, Merkle D, Middendorf M: An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. RECOMB Comparative Genomics, Volume 5267 of LNBI 2008, 143\u2013157."},{"issue":"3","key":"4813_CR21","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1016\/j.ympev.2010.03.011","volume":"55","author":"T Stach","year":"2010","unstructured":"Stach T, Braband A, Podsiadlowski L: Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis. Mol Phylogenet Evol 2010, 55(3):860\u2013870. 10.1016\/j.ympev.2010.03.011","journal-title":"Mol Phylogenet Evol"},{"issue":"Database issue","key":"4813_CR22","doi-asserted-by":"publisher","first-page":"D61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35(Database issue):D61-D65.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"4813_CR23","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1093\/bioinformatics\/btm573","volume":"24","author":"D Laslett","year":"2008","unstructured":"Laslett D, Canb\u00e4ck B: ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24(2):172\u2013175. 10.1093\/bioinformatics\/btm573","journal-title":"Bioinformatics"},{"issue":"5","key":"4813_CR24","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955\u2013964. 10.1093\/nar\/25.5.955","journal-title":"Nucleic Acids Res"},{"key":"4813_CR25","volume-title":"PhD thesis","author":"M Bernt","year":"2010","unstructured":"Bernt M: Gene order rearrangement methods for the reconstruction of phylogeny. PhD thesis. Universit\u00e4t Leipzig; 2010."},{"issue":"Suppl. 1","key":"4813_CR26","doi-asserted-by":"publisher","first-page":"i190","DOI":"10.1093\/bioinformatics\/btg1025","volume":"19","author":"JF Lefebvre","year":"2003","unstructured":"Lefebvre JF, El-Mabrouk N, Tillier E, Sankoff D: Detection and validation of single gene inversions. Bioinformatics 2003, 19(Suppl. 1):i190-i196.","journal-title":"Bioinformatics"},{"issue":"10","key":"4813_CR27","doi-asserted-by":"publisher","first-page":"1305","DOI":"10.1093\/bioinformatics\/18.10.1305","volume":"18","author":"D Sankoff","year":"2002","unstructured":"Sankoff D: Short inversions and conserved gene cluster. Bioinformatics 2002, 18(10):1305\u20131308. 10.1093\/bioinformatics\/18.10.1305","journal-title":"Bioinformatics"},{"key":"4813_CR28","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/1471-2148-8-61","volume":"8","author":"C Grande","year":"2008","unstructured":"Grande C, Templado J, Zardoya R: Evolution of gastropod mitochondrial genome arrangements. BMC Evol Biol 2008, 8: 61. 10.1186\/1471-2148-8-61","journal-title":"BMC Evol Biol"},{"key":"4813_CR29","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.toxicon.2006.04.013","volume":"48","author":"PK Bandyopadhyay","year":"2006","unstructured":"Bandyopadhyay PK, Stevenson BJ, Cady MT, Olivera BM, Wolstenholme DR: Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: Gene order and gastropod phylogeny. Toxicon 2006, 48: 29\u201343. 10.1016\/j.toxicon.2006.04.013","journal-title":"Toxicon"},{"key":"4813_CR30","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/1471-2164-7-182","volume":"7","author":"JL Boore","year":"2006","unstructured":"Boore JL: The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics 2006, 7: 182. 10.1186\/1471-2164-7-182","journal-title":"BMC Genomics"},{"issue":"1538","key":"4813_CR31","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1098\/rspb.2003.2631","volume":"271","author":"DV Lavrov","year":"2004","unstructured":"Lavrov DV, Brown WM, Boore JL: Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc Roy Soc B 2004, 271(1538):537\u2013544. 10.1098\/rspb.2003.2631","journal-title":"Proc Roy Soc B"},{"issue":"6536","key":"4813_CR32","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1038\/376163a0","volume":"376","author":"JL Boore","year":"1995","unstructured":"Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM: Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 1995, 376(6536):163\u2013165. 10.1038\/376163a0","journal-title":"Nature"},{"key":"4813_CR33","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1186\/1471-2164-9-610","volume":"9","author":"J Hua","year":"2008","unstructured":"Hua J, Li M, Dong P, Cui Y, Xie Q, Bu W: Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera). BMC Genomics 2008, 9: 610. 10.1186\/1471-2164-9-610","journal-title":"BMC Genomics"},{"issue":"7","key":"4813_CR34","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1093\/oxfordjournals.molbev.a003914","volume":"18","author":"F Nardi","year":"2001","unstructured":"Nardi F, Carapelli A, Fanciulli PP, Dallai R, Frati F: The Complete Mitochondrial DNA Sequence of the Basal Hexapod Tetrodontophora bielanensis: Evidence for Heteroplasmy and tRNA Translocations. Mol Biol Evol 2001, 18(7):1293\u20131304. 10.1093\/oxfordjournals.molbev.a003914","journal-title":"Mol Biol Evol"},{"issue":"6677","key":"4813_CR35","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/33577","volume":"392","author":"JL Boore","year":"1998","unstructured":"Boore JL, Lavrov DV, Brown WM: Gene translocation links insects and crustaceans. Nature 1998, 392(6677):667\u2013668. 10.1038\/33577","journal-title":"Nature"},{"issue":"6","key":"4813_CR36","first-page":"1259","volume":"10","author":"MF Taylor","year":"1993","unstructured":"Taylor MF, McKechnie SW, Pierce N, Kreitman M: The lepidopteran mitochondrial control region: structure and evolution. Mol Biol Evol 1993, 10(6):1259\u20131272.","journal-title":"Mol Biol Evol"},{"issue":"7","key":"4813_CR37","doi-asserted-by":"publisher","first-page":"1607","DOI":"10.1093\/molbev\/msp072","volume":"26","author":"M Dowton","year":"2009","unstructured":"Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting M: Characterization of 67 Mitochondrial tRNA Gene Rearrangements in the Hymenoptera Suggests That Mitochondrial tRNA Gene Position Is Selectively Neutral. Mol Biol Evol 2009, 26(7):1607\u20131617. 10.1093\/molbev\/msp072","journal-title":"Mol Biol Evol"},{"issue":"4","key":"4813_CR38","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1007\/s00239-003-2563-x","volume":"58","author":"E Negrisolo","year":"2004","unstructured":"Negrisolo E, Minelli A, Valle G: Extensive Gene Order Rearrangement in the Mitochondrial Genome of the Centipede Scutigera coleoptrata. J Mol Evol 2004, 58(4):413\u2013423. 10.1007\/s00239-003-2563-x","journal-title":"J Mol Evol"},{"issue":"9","key":"4813_CR39","doi-asserted-by":"publisher","first-page":"1828","DOI":"10.1093\/oxfordjournals.molbev.a003970","volume":"18","author":"R Shao","year":"2001","unstructured":"Shao R, Campbell NJH, Schmidt ER, Barker SC: Increased Rate of Gene Rearrangement in the Mitochondrial Genomes of Three Orders of Hemipteroid Insects. Mol Biol Evol 2001, 18(9):1828\u20131832. 10.1093\/oxfordjournals.molbev.a003970","journal-title":"Mol Biol Evol"},{"key":"4813_CR40","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.gene.2004.01.022","volume":"331","author":"AD Miller","year":"2004","unstructured":"Miller AD, Nguyen TTT, Burridge CP, Austin CM: Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene 2004, 331: 65\u201372.","journal-title":"Gene"},{"key":"4813_CR41","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1007\/s00239-001-0087-9","volume":"55","author":"DA Dalevi","year":"2002","unstructured":"Dalevi DA, Eriksen N, Eriksson K, Andersson SG: Measuring Genome Divergence in Bacteria: A Case Study Using Chlamydian Data. J Mol Evol 2002, 55: 24\u201336. 10.1007\/s00239-001-0087-9","journal-title":"J Mol Evol"},{"key":"4813_CR42","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/0378-1119(95)00878-0","volume":"172","author":"M Blanchette","year":"1996","unstructured":"Blanchette M, Kunisawa T, Sankoff D: Parametric genome rearrangement. Gene 1996, 172: 11\u201317.","journal-title":"Gene"},{"issue":"16","key":"4813_CR43","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/bti535","volume":"21","author":"S Yancopoulos","year":"2005","unstructured":"Yancopoulos S, Attie O, Friedberg R: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 2005, 21(16):3340\u20133346. 10.1093\/bioinformatics\/bti535","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S9-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-S9-S6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S9-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,13]],"date-time":"2024-04-13T09:28:25Z","timestamp":1713000505000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S9-S6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,5]]},"references-count":43,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4813"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s9-s6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,5]]},"article-number":"S6"}}