{"id":"https://openalex.org/W2334167823","doi":"https://doi.org/10.1093/bioinformatics/btw134","title":"GSP: a web-based platform for designing genome-specific primers in polyploids","display_name":"GSP: a web-based platform for designing genome-specific primers in polyploids","publication_year":2016,"publication_date":"2016-03-09","ids":{"openalex":"https://openalex.org/W2334167823","doi":"https://doi.org/10.1093/bioinformatics/btw134","mag":"2334167823","pmid":"https://pubmed.ncbi.nlm.nih.gov/27153733"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw134","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw134","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100630722","display_name":"Yi Wang","orcid":"https://orcid.org/0000-0002-4706-8171"},"institutions":[{"id":"https://openalex.org/I4210140558","display_name":"Western Regional Research Center","ror":"https://ror.org/03x7fn667","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210140558"]},{"id":"https://openalex.org/I4210144282","display_name":"Plant Gene Expression Center","ror":"https://ror.org/03rafms67","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210144282","https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Wang","raw_affiliation_strings":["1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA","2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210140558"]},{"raw_affiliation_string":"2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210144282"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021411613","display_name":"Vijay Tiwari","orcid":"https://orcid.org/0000-0001-7297-4048"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijay K. Tiwari","raw_affiliation_strings":["3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006806398","display_name":"Nidhi Rawat","orcid":"https://orcid.org/0000-0003-4820-0020"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nidhi Rawat","raw_affiliation_strings":["3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008626798","display_name":"Bikram S. Gill","orcid":"https://orcid.org/0000-0003-4510-9459"},"institutions":[{"id":"https://openalex.org/I189590672","display_name":"Kansas State University","ror":"https://ror.org/05p1j8758","country_code":"US","type":"education","lineage":["https://openalex.org/I189590672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bikram S. Gill","raw_affiliation_strings":["3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA","institution_ids":["https://openalex.org/I189590672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065774158","display_name":"Naxin Huo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140558","display_name":"Western Regional Research Center","ror":"https://ror.org/03x7fn667","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210140558"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naxin Huo","raw_affiliation_strings":["1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210140558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004622452","display_name":"Frank M. You","orcid":"https://orcid.org/0000-0003-4424-6179"},"institutions":[{"id":"https://openalex.org/I1331897569","display_name":"Agriculture and Agri-Food Canada","ror":"https://ror.org/051dzs374","country_code":"CA","type":"government","lineage":["https://openalex.org/I1331897569","https://openalex.org/I2802286613"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Frank M. You","raw_affiliation_strings":["4 Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada","institution_ids":["https://openalex.org/I1331897569"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086508860","display_name":"Devin Coleman\u2010Derr","orcid":"https://orcid.org/0000-0002-6282-1731"},"institutions":[{"id":"https://openalex.org/I4210144282","display_name":"Plant Gene Expression Center","ror":"https://ror.org/03rafms67","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210144282","https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Devin Coleman-Derr","raw_affiliation_strings":["2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210144282"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029670569","display_name":"Yong Gu","orcid":"https://orcid.org/0000-0002-2575-4744"},"institutions":[{"id":"https://openalex.org/I4210140558","display_name":"Western Regional Research Center","ror":"https://ror.org/03x7fn667","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210094889","https://openalex.org/I4210140558"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yong Q. Gu","raw_affiliation_strings":["1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA","institution_ids":["https://openalex.org/I4210140558"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5029670569","https://openalex.org/A5086508860"],"corresponding_institution_ids":["https://openalex.org/I4210140558","https://openalex.org/I4210144282"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.915,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.85780266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"15","first_page":"2382","last_page":"2383"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.913100004196167,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.913100004196167,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.01899999938905239,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.018699999898672104,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7437347769737244},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.6315847635269165},{"id":"https://openalex.org/keywords/polyploid","display_name":"Polyploid","score":0.6267847418785095},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.5955345630645752},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5597223043441772},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5177513957023621},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48422932624816895},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4743470251560211},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4419780373573303},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4244327247142792},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3773000240325928},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34676679968833923},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2798852026462555},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15487250685691833},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1432008147239685}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7437347769737244},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.6315847635269165},{"id":"https://openalex.org/C2776626444","wikidata":"https://www.wikidata.org/wiki/Q213410","display_name":"Polyploid","level":4,"score":0.6267847418785095},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.5955345630645752},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5597223043441772},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5177513957023621},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48422932624816895},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4743470251560211},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4419780373573303},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4244327247142792},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3773000240325928},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34676679968833923},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2798852026462555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15487250685691833},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1432008147239685},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011123","descriptor_name":"Polyploidy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw134","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw134","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27153733","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27153733","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/15/2382","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/15/2382","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1499500424","https://openalex.org/W1990813498","https://openalex.org/W1998045819","https://openalex.org/W2132926880","https://openalex.org/W2155915757","https://openalex.org/W2169486828","https://openalex.org/W6629874611"],"related_works":["https://openalex.org/W2356719812","https://openalex.org/W1992159363","https://openalex.org/W2369539772","https://openalex.org/W2924133609","https://openalex.org/W4293206821","https://openalex.org/W2366486293","https://openalex.org/W1968440560","https://openalex.org/W2367815957","https://openalex.org/W4234342421","https://openalex.org/W2909040123"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"sequences":[2,36,47,97],"among":[3],"subgenomes":[4,50],"in":[5,37,51,66],"a":[6,26,38,55,73,78,106],"polyploid":[7,39],"species":[8],"have":[9],"high":[10],"similarity,":[11],"making":[12],"it":[13],"difficult":[14],"to":[15,29,44],"design":[16,30,60,88],"genome-specific":[17,31],"primers":[18,32,61,71,94],"for":[19],"sequence":[20,57,64,74],"analysis.":[21],"RESULTS:":[22],"We":[23],"present":[24],"GSP,":[25],"web-based":[27],"platform":[28,111],"that":[33],"distinguish":[34],"subgenome":[35],"genome.":[40],"GSP":[41,90,104],"uses":[42],"BLAST":[43],"extract":[45],"homeologous":[46],"of":[48,85],"the":[49,67,86],"existing":[52],"databases,":[53],"performs":[54],"multiple":[56,96],"alignment,":[58],"and":[59,77,108,118],"based":[62],"on":[63],"variants":[65],"alignment.":[68],"An":[69],"interactive":[70],"diagram,":[72],"alignment":[75],"viewer":[76],"virtual":[79],"electrophoresis":[80],"are":[81,121,133],"displayed":[82],"as":[83],"parts":[84],"primer":[87],"result.":[89],"also":[91],"designs":[92],"specific":[93],"from":[95],"uploaded":[98],"by":[99],"users.":[100],"AVAILABILITY":[101],"AND":[102],"IMPLEMENTATION:":[103],"is":[105],"user-friendly":[107],"efficient":[109],"web":[110],"freely":[112],"accessible":[113],"at":[114,123,135],"http://probes.pw.usda.gov/GSP":[115],"Source":[116],"code":[117],"command-line":[119],"application":[120],"available":[122,134],"https://github.com/bioinfogenome/GSP":[124],"CONTACTS:":[125],"yong.gu@ars.usda.gov":[126],"or":[127],"devin.coleman-derr@ars.usda.gov":[128],"SUPPLEMENTARY":[129],"INFORMATION:":[130],"Supplementary":[131],"data":[132],"Bioinformatics":[136],"online.":[137]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-29T09:21:14.243279","created_date":"2025-10-10T00:00:00"}
