{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T08:26:02Z","timestamp":1778574362956,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2678,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated.<\/jats:p>\n               <jats:p>Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http:\/\/abacas.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0sa4@sanger.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp347","type":"journal-article","created":{"date-parts":[[2009,6,5]],"date-time":"2009-06-05T00:24:32Z","timestamp":1244161472000},"page":"1968-1969","source":"Crossref","is-referenced-by-count":407,"title":["ABACAS: algorithm-based automatic contiguation of assembled sequences"],"prefix":"10.1093","volume":"25","author":[{"given":"Samuel","family":"Assefa","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas M.","family":"Keane","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas D.","family":"Otto","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Newbold","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"},{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA and 2 Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,6,3]]},"reference":[{"key":"2023013112095494700_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":"2023013112095494700_B2","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1093\/bioinformatics\/bti091","article-title":"BACCardI\u2013a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison","volume":"21","author":"Bartels","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013112095494700_B3","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1093\/bioinformatics\/btn529","article-title":"Artemis and ACT: viewing, annotation and comparing sequences stored in relational database","volume":"24","author":"Carver","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112095494700_B4","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1093\/bioinformatics\/bth205","article-title":"Fragment assembly with short reads","volume":"20","author":"Chaisson","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112095494700_B5","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":"2023013112095494700_B6","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1093\/bioinformatics\/btm091","article-title":"Enhancements and modifications of primer design program Primer3","volume":"23","author":"Koressaar","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013112095494700_B7","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":"2023013112095494700_B8","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","article-title":"The impact of next-generation sequencing technology on genetics","volume":"24","author":"Mardis","year":"2008","journal-title":"Trends Genet."},{"key":"2023013112095494700_B9","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1093\/bioinformatics\/btn548","article-title":"Aggressive assembly of pyrosequencing reads with mates","volume":"24","author":"Miller","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112095494700_B10","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1101\/gr.1536204","article-title":"Hierarchical scaffolding with Bambus","volume":"14","author":"Pop","year":"2004","journal-title":"Genome Res."},{"key":"2023013112095494700_B11","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1093\/bioinformatics\/btm153","article-title":"OSLay: optimal syntenic layout of unfinished assemblies","volume":"23","author":"Richter","year":"2007","journal-title":"Bioinformatics"},{"issue":"Web Server issues","key":"2023013112095494700_B12","doi-asserted-by":"crossref","first-page":"W560","DOI":"10.1093\/nar\/gki356","article-title":"Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies","volume":"33","author":"van Hijum","year":"2005","journal-title":"Nucleic Acid Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1968\/48994256\/bioinformatics_25_15_1968.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1968\/48994256\/bioinformatics_25_15_1968.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:31:02Z","timestamp":1675200662000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/15\/1968\/213094"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,3]]},"references-count":12,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2009,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp347","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,8,1]]},"published":{"date-parts":[[2009,6,3]]}}}