{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:39:45Z","timestamp":1773272385121,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.<\/jats:p>\n               <jats:p>Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.<\/jats:p>\n               <jats:p>Availability: OSLay is freely available from: http:\/\/www-ab.informatik.unituebingen.de\/software\/oslay<\/jats:p>\n               <jats:p>Contact: drichter@informatik.uni-tuebingen.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm153","type":"journal-article","created":{"date-parts":[[2007,4,27]],"date-time":"2007-04-27T00:29:34Z","timestamp":1177633774000},"page":"1573-1579","source":"Crossref","is-referenced-by-count":74,"title":["OSLay: optimal syntenic layout of unfinished assemblies"],"prefix":"10.1093","volume":"23","author":[{"given":"Daniel C.","family":"Richter","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics (ZBIT), Institute for Computer Science, T\u00fcbingen University, 72076 T\u00fcbingen, Germany and 2Penn State University, Center for Comparative Genomics and Bioinformatics, University Park, PA 16802, USA"}]},{"given":"Stephan C.","family":"Schuster","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics (ZBIT), Institute for Computer Science, T\u00fcbingen University, 72076 T\u00fcbingen, Germany and 2Penn State University, Center for Comparative Genomics and Bioinformatics, University Park, PA 16802, USA"}]},{"given":"Daniel H.","family":"Huson","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics (ZBIT), Institute for Computer Science, T\u00fcbingen University, 72076 T\u00fcbingen, Germany and 2Penn State University, Center for Comparative Genomics and Bioinformatics, University Park, PA 16802, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,4,26]]},"reference":[{"key":"2023062708444224800_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023062708444224800_B2","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/bioinformatics\/bti091","article-title":"BACCardI \u2013 a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison","volume":"21","author":"Bartels","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062708444224800_B3","first-page":"375","article-title":"A meta-viewer for biomolecular data","volume":"1","author":"Delgado-Friedrichs","year":"2003","journal-title":"GI Jahrestagung"},{"key":"2023062708444224800_B4","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1093\/bioinformatics\/btg490","article-title":"CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects","volume":"20","author":"Frangeul","year":"2004","journal-title":"Bioinformatics"},{"key":"2023062708444224800_B5","article-title":"Syntenic Layout of Two Related Genomes. Proceedings of GCB 2004","author":"Friedrichs","year":"2004"},{"key":"2023062708444224800_B6","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1145\/321941.321942","article-title":"An efficient implementation of Edmond's algorithm for maximum matching on graphs","volume":"23","author":"Gabow","year":"1976","journal-title":"J. ACM"},{"key":"2023062708444224800_B7","volume-title":"Computers and Intractability: a guide to the theory of NP-completeness","author":"Garey","year":"1979"},{"key":"2023062708444224800_B8","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1101\/gr.8.3.195","article-title":"Consed: a graphical tool for sequence finishing","volume":"8","author":"Gordon","year":"1998","journal-title":"Genome Res"},{"key":"2023062708444224800_B9","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"2023062708444224800_B10","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"2023062708444224800_B11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1109\/5992.764214","article-title":"Whole-genome DNA sequencing","volume":"3","author":"Myers","year":"1999","journal-title":"IEEE Comput. Eng. Sci"},{"key":"2023062708444224800_B12","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1126\/science.1093027","article-title":"A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective","volume":"303","author":"Rendulic","year":"2004","journal-title":"Science"},{"key":"2023062708444224800_B13","first-page":"104","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"24","author":"Sanger","year":"1977","journal-title":"Biotechnology"},{"key":"2023062708444224800_B14","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/0022-2836(82)90546-0","article-title":"Nucleotide sequence of bacteriophage \u03bb DNA","volume":"162","author":"Sanger","year":"1982","journal-title":"J. Mol. Biol"},{"key":"2023062708444224800_B15","unstructured":"Smit\n              AFA\n            \n            et al.\n          \n          RepeatMasker Open-3.0\n          1996\n          &lt;http:\/\/www.repeatmasker.org&gt;"},{"key":"2023062708444224800_B16","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1093\/nar\/gki356","article-title":"Projector2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies","volume":"33","author":"van Hijum","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023062708444224800_B17","doi-asserted-by":"crossref","first-page":"8107","DOI":"10.1073\/pnas.0510740103","article-title":"Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor","volume":"103","author":"Velicer","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023062708444224800_B18","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1093\/bioinformatics\/bti122","article-title":"MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly","volume":"21","author":"Xu","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062708444224800_B19","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1093\/bioinformatics\/18.5.661","article-title":"PGAAS: a prokaryotic genome assembly assistant system","volume":"18","author":"Yu","year":"2005","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/1573\/50715484\/bioinformatics_23_13_1573.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/13\/1573\/50715484\/bioinformatics_23_13_1573.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T08:45:48Z","timestamp":1687855548000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/13\/1573\/222742"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,4,26]]},"references-count":19,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2007,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm153","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,7]]},"published":{"date-parts":[[2007,4,26]]}}}