{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T06:45:12Z","timestamp":1791096312601,"version":"4.1.0"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivations: Recent progress in ancient DNA sequencing technologies and protocols has lead to the sequencing of whole ancient bacterial genomes, as illustrated by the recent sequence of the Yersinia pestis strain that caused the Black Death pandemic. However, sequencing ancient genomes raises specific problems, because of the decay and fragmentation of ancient DNA among others, making the scaffolding of ancient contigs challenging.<\/jats:p>\n               <jats:p>Results: We show that computational paleogenomics methods aimed at reconstructing the organization of ancestral genomes from the comparison of extant genomes can be adapted to correct, order and orient ancient bacterial contigs. We describe the method FPSAC (fast phylogenetic scaffolding of ancient contigs) and apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome. We obtain a unique scaffold for the whole chromosome of this ancient genome that allows to gain precise insights into the structural evolution of the Yersinia clade.<\/jats:p>\n               <jats:p>Availability and Implementation: Code, data and results are available at http:\/\/paleogenomics.irmacs.sfu.ca\/FPSAC.<\/jats:p>\n               <jats:p>Contact: \u00a0cedric.chauve@sfu.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt527","type":"journal-article","created":{"date-parts":[[2013,9,26]],"date-time":"2013-09-26T00:24:44Z","timestamp":1380155084000},"page":"2987-2994","source":"Crossref","is-referenced-by-count":32,"title":["FPSAC: fast phylogenetic scaffolding of ancient contigs"],"prefix":"10.1093","volume":"29","author":[{"given":"Ashok","family":"Rajaraman","sequence":"first","affiliation":[{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"},{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Tannier","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"},{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cedric","family":"Chauve","sequence":"additional","affiliation":[{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"},{"name":"1 Department of Mathematics, Simon Fraser University, Burnaby (BC) V5A1S6, Canada, 2International Graduate Training Center in Mathematical Biology, Pacific Institute for the Mathematical Sciences, Vancouver (BC), Canada, 3INRIA Grenoble Rh\u00f4ne-Alpes, Montbonnot 38334, France, 4Universit\u00e9 de Lyon 1, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, CNRS UMR5558 F-69622 Villeurbanne, France and 5LaBRI, Universit\u00e9 Bordeaux I, 33405 Talence, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,10,4]]},"reference":[{"key":"2023012810490148200_btt527-B1","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1101\/gr.082784.108","article-title":"Breakpoint graphs and ancestral genome reconstructions","volume":"19","author":"Alekseyev","year":"2009","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B2","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","article-title":"Mugsy: fast multiple alignment of closely related whole genomes","volume":"27","author":"Angiuoli","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B3","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/nbt.2288","article-title":"A hybrid approach for the automated finishing of bacterial genomes","volume":"30","author":"Bashir","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2023012810490148200_btt527-B4","doi-asserted-by":"crossref","first-page":"i382","DOI":"10.1093\/bioinformatics\/bts374","article-title":"Evolution of gene neighborhoods within reconciled phylogenies","volume":"28","author":"B\u00e9rard","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B5","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-15294-8_7","article-title":"Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss","volume-title":"Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings, volume 6293 of Lecture Notes in Bioinformatics","author":"Bertrand","year":"2010"},{"key":"2023012810490148200_btt527-B6","doi-asserted-by":"crossref","first-page":"2412","DOI":"10.1101\/gr.2800104","article-title":"Reconstructing large regions of an ancestral mammalian genome in silico","volume":"14","author":"Blanchette","year":"2004","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B7","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature10549","article-title":"A draft genome of Yersinia pestis from victims of the Black Death","volume":"478","author":"Bos","year":"2011","journal-title":"Nature"},{"key":"2023012810490148200_btt527-B8","doi-asserted-by":"crossref","first-page":"13826","DOI":"10.1073\/pnas.0404012101","article-title":"Insights into the evolution of Yersinia pestis through whole-genome comparison with yersinia pseudotuberculosis","volume":"101","author":"Chain","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810490148200_btt527-B9","doi-asserted-by":"crossref","first-page":"e23501","DOI":"10.1371\/journal.pone.0023501","article-title":"Meraculous: De novo genome assembly with short paired-end reads","volume":"6","author":"Chapman","year":"2011","journal-title":"PLoS One"},{"key":"2023012810490148200_btt527-B10","doi-asserted-by":"crossref","first-page":"e1000234","DOI":"10.1371\/journal.pcbi.1000234","article-title":"A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes","volume":"4","author":"Chauve","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023012810490148200_btt527-B11","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1089\/cmb.2010.0092","article-title":"Yeast ancestral genome reconstructions: the possibilities of computational methods II","volume":"17","author":"Chauve","year":"2010","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B12","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-45278-9_37","article-title":"Hypergraph covering problems motivated by genome assembly questions (short abstract). To appear in the proceedings of","author":"Chauve","year":"2013","journal-title":"International Workshop On Combinatorial Algorithms"},{"key":"2023012810490148200_btt527-B13","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1093\/bioinformatics\/btq549","article-title":"Gloome: gain loss mapping engine","volume":"26","author":"Cohen","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B14","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1093\/bioinformatics\/btq315","article-title":"Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood","volume":"26","author":"Csur\u00f6s","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B15","doi-asserted-by":"crossref","first-page":"e1000128","DOI":"10.1371\/journal.pgen.1000128","article-title":"Dynamics of genome rearrangement in bacterial populations","volume":"4","author":"Darling","year":"2008","journal-title":"PLoS Genet."},{"key":"2023012810490148200_btt527-B16","doi-asserted-by":"crossref","first-page":"4601","DOI":"10.1128\/JB.184.16.4601-4611.2002","article-title":"Genome sequence of Yersinia pestis KIM","volume":"184","author":"Deng","year":"2002","journal-title":"J. Bacteriol."},{"key":"2023012810490148200_btt527-B17","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1093\/bioinformatics\/btp600","article-title":"Ancestors 1.0: a web server for ancestral sequence reconstruction","volume":"26","author":"Diallo","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B18","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/S1473-3099(11)70093-7","article-title":"Palaegenomics of Mycobacterium tuberculosis: epidemic burst with a degrading genome","volume":"11","author":"Djelouadji","year":"2011","journal-title":"Lancet Infect. Dis."},{"key":"2023012810490148200_btt527-B19","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1093\/bioinformatics\/bts716","article-title":"Scarpa: scaffolding reads with practical algorithms","volume":"29","author":"Donmez","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B20","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1111\/j.1469-0691.2011.03554.x","article-title":"Insights gained from paleomicrobiology into ancient and modern tuberculosis","volume":"17","author":"Donoghue","year":"2011","journal-title":"Clin. Microbiol. Infect."},{"key":"2023012810490148200_btt527-B21","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1098\/rspb.2005.3261","article-title":"Pathogenic microbial ancient DNA: a problem or an opportunity","volume":"273","author":"Donoghue","year":"2006","journal-title":"Proc. R. Soc. B"},{"key":"2023012810490148200_btt527-B22","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1111\/j.1469-0691.2012.03774.x","article-title":"Plague in the genomic area","volume":"18","author":"Drancourt","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"2023012810490148200_btt527-B23","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/nrmicro1063","article-title":"Palaemicrobiology: current issues and perspectives","volume":"3","author":"Drancourt","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"2023012810490148200_btt527-B24","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"Muscle: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012810490148200_btt527-B25","doi-asserted-by":"crossref","first-page":"406","DOI":"10.2307\/2412116","article-title":"Toward defining the course of evolution: minimum change for a specified tree topology","volume":"20","author":"Fitch","year":"1971","journal-title":"Syst. Zool."},{"key":"2023012810490148200_btt527-B26","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1093\/bioinformatics\/btm070","article-title":"Phylogenetic exploration of bacterial genomic rearrangements","volume":"23","author":"Fremez","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B27","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1089\/cmb.2011.0170","article-title":"Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences","volume":"18","author":"Gao","year":"2011","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B28","doi-asserted-by":"crossref","first-page":"R88","DOI":"10.1186\/gb-2009-10-8-r88","article-title":"Assisted assembly: how to improve a de novo genome assembly by using related species","volume":"10","author":"Gnerre","year":"2009","journal-title":"Genome Biol."},{"key":"2023012810490148200_btt527-B29","doi-asserted-by":"crossref","first-page":"e1000485","DOI":"10.1371\/journal.pgen.1000485","article-title":"Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern saccharomyces cerevisiae genome","volume":"5","author":"Gordon","year":"2009","journal-title":"PLoS Genet."},{"key":"2023012810490148200_btt527-B30","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1748-7188-5-3","article-title":"Phylogenetic comparative assembly","volume":"5","author":"Husemann","year":"2010","journal-title":"Algorithms Mol. Biol."},{"key":"2023012810490148200_btt527-B31","doi-asserted-by":"crossref","first-page":"2388","DOI":"10.1093\/bioinformatics\/bts457","article-title":"ANGES: Reconstructing ancestral genomes maps","volume":"28","author":"Jones","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B32","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1073\/pnas.1220349110","article-title":"Reference-assisted chromosome assembly","volume":"110","author":"Kim","year":"2013","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810490148200_btt527-B33","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B34","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780199299188.001.0001","volume-title":"Ancestral Sequence Reconstruction","author":"Liberles","year":"2007"},{"key":"2023012810490148200_btt527-B35","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/1471-2105-13-189","article-title":"AGORA: Assembly guided by optical restriction alignment","volume":"13","author":"Lin","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012810490148200_btt527-B36","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1101\/gr.5383506","article-title":"Reconstructing contiguous regions of an ancestral genome","volume":"16","author":"Ma","year":"2006","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B37","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1089\/cmb.2008.0069","article-title":"Dupcar: reconstructing contiguous ancestral regions with duplications","volume":"15","author":"Ma","year":"2008","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B38","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-13-S19-S11","article-title":"Linearization of ancestral multichromosomal genomes","volume":"13","author":"Manuch","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012810490148200_btt527-B39","doi-asserted-by":"crossref","first-page":"3012","DOI":"10.1093\/bioinformatics\/btq574","article-title":"Bayesian sampling of genomic rearrangement scenarios via double cut and join","volume":"26","author":"Mikl\u00f3s","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B40","author":"Minkin","year":"2013"},{"key":"2023012810490148200_btt527-B41","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1093\/bioinformatics\/btq079","article-title":"Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes","volume":"26","author":"Muffato","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B42","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1186\/1471-2105-11-304","article-title":"Scaffold filling, contig fusion and comparative gene order inference","volume":"11","author":"Munoz","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012810490148200_btt527-B43","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1101\/gr.109744.110","article-title":"Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution","volume":"20","author":"Murat","year":"2010","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B44","doi-asserted-by":"crossref","first-page":"2664","DOI":"10.1093\/bioinformatics\/btr461","article-title":"Reconstructing the architecture of the ancestral amniote genome","volume":"27","author":"Ouangraoua","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B45","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1186\/gb-2011-12-10-230","article-title":"Bacterial epidemiology and biology - lessons from genome sequencing","volume":"12","author":"Parkhill","year":"2011","journal-title":"Genome Biol."},{"key":"2023012810490148200_btt527-B46","doi-asserted-by":"crossref","first-page":"13272","DOI":"10.1073\/pnas.1121464109","article-title":"Scaling metagenome sequence assembly with probabilistic de bruijn graphs","volume":"109","author":"Pell","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810490148200_btt527-B47","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1126\/science.1139158","article-title":"Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization","volume":"317","author":"Putnam","year":"2007","journal-title":"Science"},{"key":"2023012810490148200_btt527-B48","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1101\/gr.141515.112","article-title":"Finished bacterial genomes from shotgun sequence data","volume":"22","author":"Ribeiro","year":"2012","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B49","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1093\/bioinformatics\/btp356","article-title":"Reordering contigs of draft genomes using the mauve aligner","volume":"25","author":"Rissman","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B50","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1089\/cmb.2011.0263","article-title":"Sliq: Simple linear inequalities for efficient contig scaffolding","volume":"19","author":"Roy","year":"2012","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B51","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1093\/bioinformatics\/btr562","article-title":"Fast scaffolding with small independent mixed integer programs","volume":"27","author":"Salmela","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810490148200_btt527-B52","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1089\/cmb.2009.0103","article-title":"Towards improved reconstruction of ancestral gene order in angiosperm phylogeny","volume":"16","author":"Sankoff","year":"2009","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B53","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/1471-2164-13-178","article-title":"Improving ancient DNA read mapping against modern reference genomes","volume":"13","author":"Schubert","year":"2012","journal-title":"BMC Genomics"},{"key":"2023012810490148200_btt527-B54","doi-asserted-by":"crossref","first-page":"E746","DOI":"10.1073\/pnas.1105107108","article-title":"Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the black death","volume":"108","author":"Schuenemann","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810490148200_btt527-B55","doi-asserted-by":"crossref","first-page":"17513","DOI":"10.1073\/pnas.1202997109","article-title":"Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations","volume":"109","author":"Sz\u00f6ll\u0151si","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810490148200_btt527-B56","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrg3117","article-title":"Repetitive DNA and next-generation sequencing: computational challenges and solutions","volume":"13","author":"Treangen","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"2023012810490148200_btt527-B57","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1016\/j.jtbi.2005.08.013","article-title":"Reconstruction of ancient genome and gene order from complete microbial genome sequences","volume":"239","author":"Wang","year":"2006","journal-title":"J. Theoret. Biol."},{"key":"2023012810490148200_btt527-B58","doi-asserted-by":"crossref","first-page":"e1002874","DOI":"10.1371\/journal.ppat.1002874","article-title":"Insights from genomics into bacterial pathogen populations","volume":"8","author":"Wilson","year":"2012","journal-title":"PLoS Pathog."},{"key":"2023012810490148200_btt527-B59","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1089\/cmb.2011.0083","article-title":"Consistency of sequence-based gene clusters","volume":"18","author":"Wittler","year":"2011","journal-title":"J. Comput. Biol."},{"key":"2023012810490148200_btt527-B60","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"2023012810490148200_btt527-B61","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning DNA sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/23\/2987\/48896476\/bioinformatics_29_23_2987.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/23\/2987\/48896476\/bioinformatics_29_23_2987.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:50:13Z","timestamp":1674910213000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/23\/2987\/247022"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10,4]]},"references-count":61,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2013,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt527","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,12,1]]},"published":{"date-parts":[[2013,10,4]]}}}