{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T12:37:08Z","timestamp":1780403828017,"version":"3.54.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis.<\/jats:p>\n               <jats:p>Results: We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users.<\/jats:p>\n               <jats:p>Availability and implementation: GSP is a user-friendly and efficient web platform freely accessible at http:\/\/probes.pw.usda.gov\/GSP. Source code and command-line application are available at https:\/\/github.com\/bioinfogenome\/GSP.<\/jats:p>\n               <jats:p>Contacts: \u00a0yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw134","type":"journal-article","created":{"date-parts":[[2016,3,11]],"date-time":"2016-03-11T01:49:10Z","timestamp":1457660950000},"page":"2382-2383","source":"Crossref","is-referenced-by-count":39,"title":["GSP: a web-based platform for designing genome-specific primers in polyploids"],"prefix":"10.1093","volume":"32","author":[{"given":"Yi","family":"Wang","sequence":"first","affiliation":[{"name":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA"},{"name":"2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay K.","family":"Tiwari","sequence":"additional","affiliation":[{"name":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nidhi","family":"Rawat","sequence":"additional","affiliation":[{"name":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bikram S.","family":"Gill","sequence":"additional","affiliation":[{"name":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naxin","family":"Huo","sequence":"additional","affiliation":[{"name":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank M.","family":"You","sequence":"additional","affiliation":[{"name":"4 Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin","family":"Coleman-Derr","sequence":"additional","affiliation":[{"name":"2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong Q.","family":"Gu","sequence":"additional","affiliation":[{"name":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,3,9]]},"reference":[{"key":"2023020112473398400_btw134-B1","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":"2023020112473398400_btw134-B2","doi-asserted-by":"crossref","first-page":"140.","DOI":"10.1186\/1756-0500-3-140","article-title":"Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples","volume":"3","author":"Huang","year":"2010","journal-title":"BMC Res. Notes"},{"key":"2023020112473398400_btw134-B3","doi-asserted-by":"crossref","first-page":"1251788.","DOI":"10.1126\/science.1251788","article-title":"A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome","volume":"345","author":"International Wheat Genome Sequencing, C","year":"2014","journal-title":"Science"},{"key":"2023020112473398400_btw134-B4","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s13007-015-0082-6","article-title":"A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.)","volume":"11","author":"Ma","year":"2015","journal-title":"Plant Methods"},{"key":"2023020112473398400_btw134-B5","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1093\/bioinformatics\/btv069","article-title":"PolyMarker: a fast polyploid primer design pipeline","volume":"31","author":"Ramirez-Gonzalez","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020112473398400_btw134-B6","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume":"132","author":"Rozen","year":"2000","journal-title":"Methods Mol. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/15\/2382\/49020270\/bioinformatics_32_15_2382.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/15\/2382\/49020270\/bioinformatics_32_15_2382.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:50:42Z","timestamp":1675291842000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/15\/2382\/1743425"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,9]]},"references-count":6,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2016,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw134","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,8,1]]},"published":{"date-parts":[[2016,3,9]]}}}