{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T01:22:37Z","timestamp":1771982557083,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,3,21]],"date-time":"2018-03-21T00:00:00Z","timestamp":1521590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"CALMIP","award":["P1434"],"award-info":[{"award-number":["P1434"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Segmental Duplications (SDs) are DNA fragments longer than 1 kbp, distributed within and between chromosomes and sharing more than 90% identity. Although they hold a significant role in genomic fluidity and adaptability, many key questions about their intrinsic characteristics and mutability remain unsolved due to the persistent difficulty of sequencing highly duplicated genomic regions. The recent development of long and linked-read NGS technologies will increase the need to search for SDs in genomes newly sequenced with these technics. The main limitation of SD analysis will soon be the availability of efficient detection software, to retrieve and compare SD genomic component between species or lineages.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we present the open-source ASGART, \u2018A Segmental duplications Gathering And Refining Tool\u2019, developed to search for segmental duplications (SDs) in any assembled sequence. We have tested and benchmarked ASGART on five models organisms. Our results demonstrate ASGART\u2019s ability to extract SDs from any genome-wide sequence, regardless of genomic size or organizational complexity and quicker than any other software available.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The online version of ASGART is available at http:\/\/asgart.irit.fr. The source code of ASGART is available both on the ASGART website and at https:\/\/github.com\/delehef\/asgart.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty172","type":"journal-article","created":{"date-parts":[[2018,3,20]],"date-time":"2018-03-20T20:24:48Z","timestamp":1521577488000},"page":"2708-2714","source":"Crossref","is-referenced-by-count":24,"title":["ASGART: fast and parallel genome scale segmental duplications mapping"],"prefix":"10.1093","volume":"34","author":[{"given":"Franklin","family":"Delehelle","sequence":"first","affiliation":[{"name":"UMR5505 \u2013 CNRS-Universit\u00e9 de Toulouse, Institut de Recherche en Informatique de Toulouse (IRIT), Toulouse, France"},{"name":"UMR 5288 \u2013 AMIS Universit\u00e9 Paul Sabatier\/CNRS, Facult\u00e9 de M\u00e9decine Purpan, Toulouse, France"}]},{"given":"Sylvain","family":"Cussat-Blanc","sequence":"additional","affiliation":[{"name":"UMR5505 \u2013 CNRS-Universit\u00e9 de Toulouse, Institut de Recherche en Informatique de Toulouse (IRIT), Toulouse, France"}]},{"given":"Jean-Marc","family":"Alliot","sequence":"additional","affiliation":[{"name":"UMR5505 \u2013 CNRS-Universit\u00e9 de Toulouse, Institut de Recherche en Informatique de Toulouse (IRIT), Toulouse, France"}]},{"given":"Herv\u00e9","family":"Luga","sequence":"additional","affiliation":[{"name":"UMR5505 \u2013 CNRS-Universit\u00e9 de Toulouse, Institut de Recherche en Informatique de Toulouse (IRIT), Toulouse, France"}]},{"given":"Patricia","family":"Balaresque","sequence":"additional","affiliation":[{"name":"UMR 5288 \u2013 AMIS Universit\u00e9 Paul Sabatier\/CNRS, Facult\u00e9 de M\u00e9decine Purpan, Toulouse, France"}]}],"member":"286","published-online":{"date-parts":[[2018,3,21]]},"reference":[{"key":"2023012712481212200_bty172-B1","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1471-2229-4-10","article-title":"The roles of segmental and tandem gene duplication in the evolution of large gene families in arabidopsis thaliana","volume":"4","author":"Cannon","year":"2004","journal-title":"BMC Plant Biol"},{"key":"2023012712481212200_bty172-B2","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/S0168-9525(01)02492-1","article-title":"Recent duplication, domain accretion and the dynamic mutation of the human genome","volume":"17","author":"Eichler","year":"2001","journal-title":"Trends Genet"},{"key":"2023012712481212200_bty172-B3","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/ng1401","article-title":"Complex snp-related sequence variation in segmental genome duplications","volume":"36","author":"Fredman","year":"2004","journal-title":"Nat. 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