{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T15:07:39Z","timestamp":1722697659128},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understanding their dynamic behavior: The data for this kind of investigation can be provided by comparative genomics of closely related organisms. The amount of data thus involved requires a strong computational effort, which should be alleviated.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our approach proposes to exploit the high similarity among homologous chromosomes of different strains of the same species, following a progressive comparative genomics philosophy. We introduce a software tool based on our new fast algorithm, called <jats:sc>regender<\/jats:sc>, which is able to identify the conserved regions between chromosomes. Our case study is represented by a unique recently available dataset of 39 different strains of <jats:italic>S.cerevisiae<\/jats:italic>, which <jats:sc>regender<\/jats:sc>\u2009is able to compare in few minutes. By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, and marking the candidate Tys based on their length, we are able to locate <jats:italic>a priori<\/jats:italic>\u2009and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putative mobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of inter-specific evolution: indeed, many events of non-conservation among different yeast strains correspond to PMEs. A clustering based on the presence\/absence of the candidate Tys in the strains suggests an evolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis, even though it is computed without using phylogenetic information.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The case study indicates that the proposed methodology brings two major advantages: (<jats:italic>a<\/jats:italic>) it does not require any template sequence for the wanted MGEs and (<jats:italic>b<\/jats:italic>) it can be applied to infer MGEs also for low coverage genomes with unresolved bases, where traditional approaches are largely ineffective.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-102","type":"journal-article","created":{"date-parts":[[2013,6,17]],"date-time":"2013-06-17T14:14:36Z","timestamp":1371478476000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Mobilomics in Saccharomyces cerevisiaestrains"],"prefix":"10.1186","volume":"14","author":[{"given":"Giulia","family":"Menconi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanni","family":"Battaglia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto","family":"Grossi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadia","family":"Pisanti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto","family":"Marangoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,3,20]]},"reference":[{"key":"5923_CR1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1007\/978-1-60327-853-9_2","volume":"532","author":"JL Siefert","year":"2009","unstructured":"Siefert JL: Defining the Mobilome. Methods Mol Biol. 2009, 532: 13-27. 10.1007\/978-1-60327-853-9_2.","journal-title":"Methods Mol Biol"},{"key":"5923_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.0014-3820.2001.tb01268.x","volume":"55","author":"MG Kidwell","year":"2001","unstructured":"Kidwell MG, Lisch DR: Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution. 2001, 55: 1-24.","journal-title":"Evolution"},{"key":"5923_CR3","first-page":"593","volume":"18","author":"V Conti","year":"2006","unstructured":"Conti V, Aghaie A, Cilli M, et al: crv4, a mouse model for humanataxia associated with kyphoscoliosis caused by an mRNA splicing mutation of the metabotropic glutamatereceptor 1 (Grm1). Int J Mol Med. 2006, 18: 593-600.","journal-title":"Int J Mol Med"},{"key":"5923_CR4","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/S0959-437X(98)80092-0","volume":"8","author":"HJ Kazazian","year":"1998","unstructured":"Kazazian HJ: Mobile elements and disease. Curr Opin Genet Dev. 1998, 8: 343-350. 10.1016\/S0959-437X(98)80092-0.","journal-title":"Curr Opin Genet Dev"},{"key":"5923_CR5","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1017\/S0016672302009710","volume":"80","author":"T Leonardo","year":"2002","unstructured":"Leonardo T, Nuzhdin S: Mobile elements and disease. Genet Res. 2002, 80: 155-161. 10.1017\/S0016672302009710.","journal-title":"Genet Res"},{"key":"5923_CR6","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1534\/genetics.105.052241","volume":"174","author":"A Le Rouzic","year":"2006","unstructured":"Le Rouzic A, Capy P: Population genetics models of competition between transposable elements sub-families. Genetics. 2006, 174: 785-793. 10.1534\/genetics.105.052241.","journal-title":"Genetics"},{"key":"5923_CR7","doi-asserted-by":"publisher","first-page":"19375","DOI":"10.1073\/pnas.0705238104","volume":"104","author":"A Le Rouzic","year":"2007","unstructured":"Le Rouzic A, Boutin TS, Capy P: Long term evolution of transposable elements. PNAS. 2007, 104: 19375-19380. 10.1073\/pnas.0705238104.","journal-title":"PNAS"},{"key":"5923_CR8","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.tig.2009.05.003","volume":"25","author":"S Venner","year":"2009","unstructured":"Venner S, Feschotte C, Biemont C: Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet. 2009, 25: 317-323. 10.1016\/j.tig.2009.05.003.","journal-title":"Trends Genet"},{"key":"5923_CR9","doi-asserted-by":"publisher","first-page":"2422","DOI":"10.1111\/j.1420-9101.2010.02106.x","volume":"23","author":"D Rankin","year":"2010","unstructured":"Rankin D, Bichsel M, Wagner A: Mobile DNA can drive lineage extinction in prokaryotic populations. J Evol Biol. 2010, 23: 2422-2431. 10.1111\/j.1420-9101.2010.02106.x.","journal-title":"J Evol Biol"},{"key":"5923_CR10","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1038\/sj.emboj.7600024","volume":"23","author":"R Koszul","year":"2004","unstructured":"Koszul R, Caburet S, Dujon B, Fischer G: Eukaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 2004, 23: 234-243. 10.1038\/sj.emboj.7600024.","journal-title":"EMBO J"},{"key":"5923_CR11","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1023\/A:1006344508454","volume":"42","author":"J Bennetzen","year":"2000","unstructured":"Bennetzen J: Transposable elements contribution to plant gene and genome evolution. Plant Mol Biol. 2000, 42: 251-269. 10.1023\/A:1006344508454.","journal-title":"Plant Mol Biol"},{"key":"5923_CR12","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1007\/s11692-007-9012-5","volume":"34","author":"L Johnson","year":"2007","unstructured":"Johnson L: The genome strikes back: the evolutionary importance of defence against mobile elements. Evo Biol. 2007, 34: 121-129. 10.1007\/s11692-007-9012-5.","journal-title":"Evo Biol"},{"key":"5923_CR13","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.gde.2009.10.013","volume":"19","author":"G Bourque","year":"2009","unstructured":"Bourque G: Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opin Genet Dev. 2009, 19: 607-612. 10.1016\/j.gde.2009.10.013.","journal-title":"Curr Opin Genet Dev"},{"key":"5923_CR14","doi-asserted-by":"publisher","first-page":"19945","DOI":"10.1073\/pnas.1014330107","volume":"107","author":"R Brittten","year":"2010","unstructured":"Brittten R: Transposable element insertions have strongly affected human evolution. PNAS. 2010, 107: 19945-19948. 10.1073\/pnas.1014330107.","journal-title":"PNAS"},{"key":"5923_CR15","doi-asserted-by":"publisher","first-page":"1626","DOI":"10.1126\/science.1089670","volume":"303","author":"HH Kazian","year":"2004","unstructured":"Kazian HH: Mobile elements: drivers of genome evolution. Science. 2004, 303: 1626-1632. 10.1126\/science.1089670.","journal-title":"Science"},{"key":"5923_CR16","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/hdy.2009.165","volume":"104","author":"E Lerat","year":"2010","unstructured":"Lerat E: Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity. 2010, 104: 520-533. 10.1038\/hdy.2009.165.","journal-title":"Heredity"},{"key":"5923_CR17","volume-title":"Discrete Appl Math","author":"M Federico","year":"2013","unstructured":"Federico M, Peterlongo P, Pisanti N, Sagot MF: RIME: Rrepeat Identification. Discrete Appl Math. 2013, in press"},{"key":"5923_CR18","doi-asserted-by":"crossref","unstructured":"Peterlongo P, Sacomoto GT, do Lago AP, Pisanti N, Sagot MF: Lossless filter for multiple repeats with bounded edit distance. Algorithms Mol Biol. 2009, 4 (3):","DOI":"10.1186\/1748-7188-4-3"},{"key":"5923_CR19","doi-asserted-by":"publisher","first-page":"e212","DOI":"10.1371\/journal.pgen.0020212","volume":"2","author":"A Gabriel","year":"2006","unstructured":"Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt S, Dunham M: Global mapping of transposon location. PLoS Genet. 2006, 2: e212-10.1371\/journal.pgen.0020212.","journal-title":"PLoS Genet"},{"key":"5923_CR20","first-page":"131","volume-title":"BIOINFORMATICS 2011: International Conference on Bioinformatics Models, Methods and Algorithms","author":"G Menconi","year":"2011","unstructured":"Menconi G, Battaglia G, Grossi R, Pisanti N, Marangoni R: Inferring mobile elements in S.cerevisiae strains. BIOINFORMATICS 2011: International Conference on Bioinformatics Models, Methods and Algorithms. 2011, SciTePress, 131-136. [ISBN: 978-989-8425-36-2]"},{"key":"5923_CR21","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/B978-012301463-4\/50005-X","volume-title":"Evol Genome","author":"M Kidwell","year":"2005","unstructured":"Kidwell M: Transposable elements. Evol Genome. 2005, : , 165-221."},{"key":"5923_CR22","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/nature07743","volume":"458","author":"G Liti","year":"2009","unstructured":"Liti G, Carter DM, Moses AM, et al: Population genomics of domestic and wild yeast. Nature. 2009, 458: 337-341. 10.1038\/nature07743.","journal-title":"Nature"},{"issue":"Database issue","key":"5923_CR23","doi-asserted-by":"publisher","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","volume":"40","author":"JM Cherry","year":"2012","unstructured":"Cherry JM, Hong EL, Amundsen C, et al: Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res. 2012, 40 (Database issue): D700-D705.","journal-title":"Nucleic Acids Res"},{"key":"5923_CR24","doi-asserted-by":"publisher","first-page":"8553","DOI":"10.1073\/pnas.84.23.8553","volume":"84","author":"H Xu","year":"1987","unstructured":"Xu H, Boeke J: High-frequency deletion between homologous sequences during retrotransposition of Ty elements in Saccharomyces cerevisiae. PNAS. 1987, 84: 8553-8557. 10.1073\/pnas.84.23.8553.","journal-title":"PNAS"},{"key":"5923_CR25","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1101\/gr.4361206","volume":"16","author":"A Caspi","year":"2006","unstructured":"Caspi A, Pachter L: Identification of transposable elements using multiple alignments of related genomes. Genome Res. 2006, 16: 260-270.","journal-title":"Genome Res"},{"key":"5923_CR26","volume-title":"Regender: Resident Genome Detector","author":"G Battaglia","year":"2010","unstructured":"Battaglia G, Menconi G, Grossi R, Pisanti N, Marangoni R: Regender: Resident Genome Detector. 2010, [http:\/\/www.di.unipi.it\/~gbattag\/regender]"},{"key":"5923_CR27","first-page":"271","volume-title":"BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms","author":"G Menconi","year":"2012","unstructured":"Menconi G, Battaglia G, Grossi R, Pisanti N, Marangoni R: A taste of yeast mobilomics. BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms. 2012, SciTePress, 271-274. [ISBN]"},{"key":"5923_CR28","unstructured":"UCSC Genome Browser. [http:\/\/genome.ucsc.edu\/]"},{"issue":"16","key":"5923_CR29","doi-asserted-by":"publisher","first-page":"3829","DOI":"10.1093\/nar\/21.16.3829","volume":"21","author":"O White","year":"1993","unstructured":"White O, Dunning T, Sutton G, Adams M, Venter JC, Fields C: A quality control algorithm for DNA sequencing projects. Nucleic Acids Res. 1993, 21 (16): 3829-3838. 10.1093\/nar\/21.16.3829.","journal-title":"Nucleic Acids Res"},{"key":"5923_CR30","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1101\/gr.2052904","volume":"14","author":"N Bachman","year":"2004","unstructured":"Bachman N, Eby Y, Boeke J: Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes. Genome Res. 2004, 14: 1232-1247. 10.1101\/gr.2052904.","journal-title":"Genome Res"},{"issue":"0","key":"5923_CR31","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1093\/gbe\/evp034","volume":"1","author":"S Di Rienzi","year":"2010","unstructured":"Di Rienzi S, Collingwood D, Raghuraman M, Brewer B: Fragile genomic sites are associated with origins of replication. Genome Biol Evol. 2010, 1 (0): 350-10.1093\/gbe\/evp034.","journal-title":"Genome Biol Evol"},{"issue":"21","key":"5923_CR32","doi-asserted-by":"publisher","first-page":"11383","DOI":"10.1073\/pnas.97.21.11383","volume":"97","author":"J Gerton","year":"2000","unstructured":"Gerton J, DeRisi J, Shroff R, Lichten M, Brown P, Petes T: Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2000, 97 (21): 11383-10.1073\/pnas.97.21.11383.","journal-title":"Proc Natl Acad Sci USA"},{"key":"5923_CR33","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/1471-2164-9-49","volume":"9","author":"A Bagshaw","year":"2008","unstructured":"Bagshaw A, Pitt J, Gemmell N: High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots. BMC Genomics. 2008, 9: 49-10.1186\/1471-2164-9-49.","journal-title":"BMC Genomics"},{"key":"5923_CR34","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/nsmb.1754","volume":"17","author":"R Szilard","year":"2010","unstructured":"Szilard R, Jacques P, Laram\u00e9e L, Cheng B, Galicia S, Bataille A, Yeung M, Mendez M, Bergeron M, Robert F, et al: Systematic identification of fragile sites via genome-wide location analysis of \u03b3-H2AX. Nat Struct Mol Biol. 2010, 17: 299-305. 10.1038\/nsmb.1754.","journal-title":"Nat Struct Mol Biol"},{"issue":"4","key":"5923_CR35","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1016\/j.molcel.2010.07.024","volume":"39","author":"D Fachinetti","year":"2010","unstructured":"Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, Shirahige K, Azvolinsky A, Zakian V, Foiani M: Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell. 2010, 39 (4): 595-605. 10.1016\/j.molcel.2010.07.024.","journal-title":"Mol Cell"},{"key":"5923_CR36","first-page":"15","volume-title":"Hand Comput Mol Biol","author":"E Ohlebusch","year":"2006","unstructured":"Ohlebusch E, Abouelhoda M: A chaining algorithms and applications in comparative genomics. Hand Comput Mol Biol. 2006, London: Chapman and Hall, 15-21."},{"key":"5923_CR37","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology","author":"D Gusfield","year":"1997","unstructured":"Gusfield D: Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. 1997, Cambridge: Cambridge University Press"},{"issue":"8","key":"5923_CR38","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1101\/gr.10.8.1115","volume":"10","author":"W Kent","year":"2000","unstructured":"Kent W, Zahler A: Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 2000, 10 (8): 1115-10.1101\/gr.10.8.1115.","journal-title":"Genome Res"},{"key":"5923_CR39","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1101\/gr.809403","volume":"13","author":"S Schwartz","year":"2003","unstructured":"Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res. 2003, 13: 103-10.1101\/gr.809403.","journal-title":"Genome Res"},{"issue":"4","key":"5923_CR40","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1101\/gr.10.4.577","volume":"10","author":"S Schwartz","year":"2000","unstructured":"Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker\u2014A web server for aligning two genomic DNA sequences. Genome Res. 2000, 10 (4): 577-10.1101\/gr.10.4.577.","journal-title":"Genome Res"},{"issue":"13","key":"5923_CR41","doi-asserted-by":"publisher","first-page":"3518","DOI":"10.1093\/nar\/gkg579","volume":"31","author":"S Schwartz","year":"2003","unstructured":"Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, et al: MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 2003, 31 (13): 3518-10.1093\/nar\/gkg579.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5923_CR42","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"W Kent","year":"2002","unstructured":"Kent W: BLAT: the BLAST-like alignment tool. Genome Res. 2002, 12 (4): 656-","journal-title":"Genome Res"},{"issue":"8","key":"5923_CR43","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1093\/bioinformatics\/14.8.715","volume":"14","author":"P Vincens","year":"1998","unstructured":"Vincens P, Buffat L, Andre C, Chevrolat J, Boisvieux J, Hazout S: A strategy for finding regions of similarity in complete genome sequences. Bioinformatics. 1998, 14 (8): 715-10.1093\/bioinformatics\/14.8.715.","journal-title":"Bioinformatics"},{"issue":"7","key":"5923_CR44","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1101\/gr.10.7.950","volume":"10","author":"S Batzoglou","year":"2000","unstructured":"Batzoglou S, Pachter L, Mesirov J, Berger B, Lander E: Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 2000, 10 (7): 950-10.1101\/gr.10.7.950.","journal-title":"Genome Res"},{"issue":"5","key":"5923_CR45","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1093\/bioinformatics\/17.5.419","volume":"17","author":"J Buhler","year":"2001","unstructured":"Buhler J: Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics. 2001, 17 (5): 419-428. 10.1093\/bioinformatics\/17.5.419.","journal-title":"Bioinformatics"},{"issue":"3","key":"5923_CR46","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1093\/bioinformatics\/18.3.440","volume":"18","author":"B Ma","year":"2002","unstructured":"Ma B, Tromp J, Li M: PatternHunter: faster and more sensitive homology search. Bioinformatics. 2002, 18 (3): 440-10.1093\/bioinformatics\/18.3.440.","journal-title":"Bioinformatics"},{"issue":"3","key":"5923_CR47","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1142\/S0219720004000661","volume":"2","author":"M Li","year":"2004","unstructured":"Li M, Ma B, Kisman D, Tromp J: Patternhunter II: highly sensitive and fast homology search. J Bioinformatics Comput Biol. 2004, 2 (3): 417-440. 10.1142\/S0219720004000661.","journal-title":"J Bioinformatics Comput Biol"},{"key":"5923_CR48","first-page":"138","volume-title":"CSB, proceedings","author":"M Brudno","year":"2002","unstructured":"Brudno M, Morgenstern B: Fast and sensitive alignment of large genomic sequences. CSB, proceedings. 2002, IEEE Computer Soc, 138-147."},{"issue":"11","key":"5923_CR49","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/nar\/27.11.2369","volume":"27","author":"A Delcher","year":"1999","unstructured":"Delcher A, Kasif S, Fleischmann R, Peterson J, White O, Salzberg S: Alignment of whole genomes. Nucleic Acids Res. 1999, 27 (11): 2369-10.1093\/nar\/27.11.2369.","journal-title":"Nucleic Acids Res"},{"key":"5923_CR50","first-page":"122","volume-title":"Proceedings of the Second Conference on Asia-Pacific bioinformatics-Volume 29","author":"J Deogun","year":"2004","unstructured":"Deogun J, Yang J, Ma F: Emagen: An efficient approach to multiple whole genome alignment. Proceedings of the Second Conference on Asia-Pacific bioinformatics-Volume 29. 2004, Australian Computer Society, Inc., 122-122."},{"key":"5923_CR51","doi-asserted-by":"publisher","first-page":"S312","DOI":"10.1093\/bioinformatics\/18.suppl_1.S312","volume":"18","author":"M H\u00f6hl","year":"2002","unstructured":"H\u00f6hl M, Kurtz S, Ohlebusch E: Efficient multiple genome alignment. Bioinformatics. 2002, 18: S312-S320. 10.1093\/bioinformatics\/18.suppl_1.S312.","journal-title":"Bioinformatics"},{"issue":"3","key":"5923_CR52","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1145\/256163.256168","volume":"15","author":"JD Cohen","year":"1997","unstructured":"Cohen JD: Recursive hashing functions for n-Grams. ACM Trans Inf Syst. 1997, 15 (3): 291-320. 10.1145\/256163.256168.","journal-title":"ACM Trans Inf Syst"},{"key":"5923_CR53","volume-title":"fastutil: Fast and compact type-specific collections for Java","author":"S Vigna","year":"2006","unstructured":"Vigna S: fastutil: Fast and compact type-specific collections for Java. 2006"},{"key":"5923_CR54","volume-title":"SciPy: Open source scientific tools for Python","author":"E Jones","year":"2001","unstructured":"Jones E, Oliphant T, Peterson P, et al: SciPy: Open source scientific tools for Python. 2001, http:\/\/www.scipy.org,"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-102.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T00:20:02Z","timestamp":1630542002000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-102"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,3,20]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5923"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-102","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,3,20]]},"assertion":[{"value":"13 November 2012","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 February 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 March 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"102"}}