{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T05:00:17Z","timestamp":1774933217055,"version":"3.50.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: We report AtPRIMER, an application that automates the discovery of new polymorphic markers between ecotypes of Arabidopsis thaliana. On specifying two ecotypes and the genomic region of interest, the script retrieves all corresponding single nucleotide polymorphisms (SNPs) and generates CAPS and\/or dCAPS PCR primer sequences. We show that AtPRIMER accurately found specific polymorphic markers for our linkage mapping project. AtPRIMER will therefore be useful for efficient marker development with high density and specificity.<\/jats:p><jats:p>Availability: This PERL\/CGI program is available for non-commercial users at http:\/\/www.AtPRIMER.tsl.ac.uk. The web-based version is available for public use at the same URL.<\/jats:p><jats:p>Contact: adnane.nemri@tsl.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm501","type":"journal-article","created":{"date-parts":[[2007,11,19]],"date-time":"2007-11-19T07:12:39Z","timestamp":1195456359000},"page":"3108-3109","source":"Crossref","is-referenced-by-count":4,"title":["Marker development for the genetic study of natural variation in<i>Arabidopsis thaliana<\/i>"],"prefix":"10.1093","volume":"23","author":[{"given":"Adnane","family":"Nemri","sequence":"first","affiliation":[{"name":"1 Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA"}]},{"given":"Michael M.","family":"Neff","sequence":"additional","affiliation":[{"name":"1 Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA"}]},{"given":"Michael","family":"Burrell","sequence":"additional","affiliation":[{"name":"1 Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA"}]},{"given":"Jonathan D.G.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA"}]},{"given":"David J.","family":"Studholme","sequence":"additional","affiliation":[{"name":"1 Sainsbury Laboratory, Norwich NR4 7UH, UK and 2Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,11,15]]},"reference":[{"key":"2023041208451461800_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1046\/j.1365-313X.1993.04020403.x","article-title":"A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific markers","volume":"4","author":"Konieczny","year":"1993","journal-title":"Plant J"},{"key":"2023041208451461800_","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1093\/bioinformatics\/bth254","article-title":"PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR","volume":"20","author":"Marshall","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041208451461800_","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1046\/j.1365-313X.1998.00124.x","article-title":"dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics","volume":"14","author":"Neff","year":"1998","journal-title":"Plant J."},{"key":"2023041208451461800_","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/S0168-9525(02)02820-2","article-title":"Web-based primer design for single nucleotide polymorphism analysis","volume":"18","author":"Neff","year":"2002","journal-title":"Trends Genet."},{"key":"2023041208451461800_","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1371\/journal.pbio.0030196","article-title":"The pattern of polymorphism in Arabidopsis thaliana","volume":"3","author":"Nordborg","year":"2005","journal-title":"PLoS Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/22\/3108\/49857870\/bioinformatics_23_22_3108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/22\/3108\/49857870\/bioinformatics_23_22_3108.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T20:47:17Z","timestamp":1684097237000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/22\/3108\/209584"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,15]]},"references-count":5,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2007,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm501","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,11,15]]},"published":{"date-parts":[[2007,11,15]]}}}