{"id":"https://openalex.org/W2909989938","doi":"https://doi.org/10.1093/bioinformatics/btz004","title":"KASPspoon: an <i>in\u00a0vitro</i> and <i>in silico</i> PCR analysis tool for high-throughput SNP genotyping","display_name":"KASPspoon: an <i>in\u00a0vitro</i> and <i>in silico</i> PCR analysis tool for high-throughput SNP genotyping","publication_year":2019,"publication_date":"2019-01-04","ids":{"openalex":"https://openalex.org/W2909989938","doi":"https://doi.org/10.1093/bioinformatics/btz004","mag":"2909989938","pmid":"https://pubmed.ncbi.nlm.nih.gov/30624621"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/17/3187/29592001/btz004.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/17/3187/29592001/btz004.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083340569","display_name":"Alsamman M. Alsamman","orcid":"https://orcid.org/0000-0002-7765-5035"},"institutions":[{"id":"https://openalex.org/I4210129354","display_name":"Agricultural Genetic Engineering Research Institute","ror":"https://ror.org/038d53f16","country_code":"EG","type":"facility","lineage":["https://openalex.org/I4210129354"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Alsamman M Alsamman","raw_affiliation_strings":["Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103252297","display_name":"Shafik D. Ibrahim","orcid":"https://orcid.org/0000-0001-8152-1999"},"institutions":[{"id":"https://openalex.org/I4210129354","display_name":"Agricultural Genetic Engineering Research Institute","ror":"https://ror.org/038d53f16","country_code":"EG","type":"facility","lineage":["https://openalex.org/I4210129354"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Shafik D Ibrahim","raw_affiliation_strings":["Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073070519","display_name":"Aladdin Hamwieh","orcid":"https://orcid.org/0000-0001-6060-5560"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Aladdin Hamwieh","raw_affiliation_strings":["International Center for Agricultural Research in the Dry Areas (ICARDA) Department of Biotechnology, , Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"International Center for Agricultural Research in the Dry Areas (ICARDA) Department of Biotechnology, , Cairo, Egypt","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073070519","https://openalex.org/A5083340569"],"corresponding_institution_ids":["https://openalex.org/I4210129354"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7294,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.84608457,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"17","first_page":"3187","last_page":"3190"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.8690000176429749,"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"}},"topics":[{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.8690000176429749,"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"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.10830000042915344,"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"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.004100000020116568,"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/in-silico","display_name":"In silico","score":0.8182774782180786},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.6573238372802734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6520594358444214},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.609991192817688},{"id":"https://openalex.org/keywords/snp-genotyping","display_name":"SNP genotyping","score":0.5858244299888611},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.557205855846405},{"id":"https://openalex.org/keywords/quantitative-trait-locus","display_name":"Quantitative trait locus","score":0.4890792965888977},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.4888881742954254},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46089428663253784},{"id":"https://openalex.org/keywords/molecular-inversion-probe","display_name":"Molecular Inversion Probe","score":0.4525160789489746},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.4511878788471222},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.420663058757782},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3608347177505493},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.32512786984443665}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8182774782180786},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6573238372802734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6520594358444214},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.609991192817688},{"id":"https://openalex.org/C163691529","wikidata":"https://www.wikidata.org/wiki/Q7391886","display_name":"SNP genotyping","level":5,"score":0.5858244299888611},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.557205855846405},{"id":"https://openalex.org/C81941488","wikidata":"https://www.wikidata.org/wiki/Q853421","display_name":"Quantitative trait locus","level":3,"score":0.4890792965888977},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.4888881742954254},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46089428663253784},{"id":"https://openalex.org/C59701697","wikidata":"https://www.wikidata.org/wiki/Q6895959","display_name":"Molecular Inversion Probe","level":5,"score":0.4525160789489746},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.4511878788471222},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.420663058757782},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3608347177505493},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.32512786984443665},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018895","descriptor_name":"Microsatellite Repeats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040641","descriptor_name":"Quantitative Trait Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/17/3187/29592001/btz004.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30624621","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30624621","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:europepmc.org:5704513","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6735863","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/17/3187/29592001/btz004.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320420","display_name":"Grains Research and Development Corporation","ror":"https://ror.org/02xwr1996"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1536229846","https://openalex.org/W1926675790","https://openalex.org/W1986106281","https://openalex.org/W1996423252","https://openalex.org/W2032019813","https://openalex.org/W2104287544","https://openalex.org/W2106415954","https://openalex.org/W2106578986","https://openalex.org/W2108800326","https://openalex.org/W2158804744","https://openalex.org/W2162098634","https://openalex.org/W2399909957","https://openalex.org/W2528840539","https://openalex.org/W2802953232","https://openalex.org/W4232707558"],"related_works":["https://openalex.org/W2414446413","https://openalex.org/W1504890006","https://openalex.org/W3139651602","https://openalex.org/W2936024166","https://openalex.org/W2783076127","https://openalex.org/W2341307294","https://openalex.org/W2026621123","https://openalex.org/W2062373810","https://openalex.org/W2104756498","https://openalex.org/W2050613846"],"abstract_inverted_index":{"MOTIVATION:":[0],"Fine":[1],"mapping":[2,12],"becomes":[3],"a":[4,72,89],"routine":[5,73],"trial":[6],"following":[7],"quantitative":[8],"trait":[9],"loci":[10,55],"(QTL)":[11],"studies":[13],"to":[14,119,138,166,171,184,199],"shrink":[15],"the":[16,32,102,140,155,190],"size":[17],"of":[18,26,34,45,53,58,192],"genomic":[19,43],"segments":[20,44],"underlying":[21],"causal":[22],"variants.":[23],"The":[24],"availability":[25],"whole":[27],"genome":[28,158],"sequences":[29],"can":[30],"facilitate":[31],"development":[33],"high":[35],"marker":[36],"density":[37],"and":[38,50,64,74,105,110,125,133,150,153,183,194,212],"predict":[39],"gene":[40,145],"content":[41],"in":[42,108,111,131,134,210,213],"interest.":[46],"Correlations":[47],"between":[48,130],"genetic":[49,61,151],"physical":[51,149],"positions":[52],"these":[54],"require":[56],"handling":[57],"different":[59,209],"experimental":[60],"data":[62,229],"types,":[63],"ultimately":[65],"converting":[66],"them":[67],"into":[68,83,179],"positioning":[69],"markers":[70,82,178],"using":[71],"efficient":[75],"tool.":[76],"RESULTS:":[77],"To":[78],"convert":[79,172],"classical":[80,176],"QTL":[81,173],"KASP":[84,168],"assay":[85,169],"primers,":[86],"KASPspoon":[87,115,147,162,203],"simulates":[88],"PCR":[90,113,136],"by":[91,175],"running":[92],"an":[93],"approximate-match":[94],"searching":[95],"analysis":[96],"on":[97],"user-entered":[98],"primer":[99,156],"pairs":[100],"against":[101],"provided":[103],"sequences,":[104],"then":[106],"comparing":[107],"vitro":[109,132,214],"silico":[112,135,211],"results.":[114,215],"reports":[116,154],"amplimers":[117,143],"close":[118],"or":[120],"adjoining":[121],"genes/SNPs/simple":[122],"sequence":[123],"repeats":[124],"those":[126],"that":[127,207],"are":[128,230],"shared":[129],"results":[137],"select":[139],"most":[141],"appropriate":[142],"for":[144,160,189],"discovery.":[146],"compares":[148],"maps,":[152],"set":[157],"coverage":[159],"PCR-walking.":[161],"could":[163],"be":[164],"used":[165],"design":[167],"primers":[170],"acquired":[174],"molecular":[177],"high-throughput":[180],"genotyping":[181],"assays":[182],"provide":[185],"major":[186],"SNP":[187],"resource":[188],"dissection":[191],"genotypic":[193],"phenotypic":[195],"variation.":[196],"In":[197],"addition":[198],"human-readable":[200],"output":[201],"files,":[202],"creates":[204],"Circos":[205],"configurations":[206],"illustrate":[208],"AVAILABILITY":[216],"AND":[217],"IMPLEMENTATION:":[218],"Code":[219],"available":[220,231],"under":[221],"GNU":[222],"GPL":[223],"at":[224,232],"(http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon).":[225],"SUPPLEMENTARY":[226],"INFORMATION:":[227],"Supplementary":[228],"Bioinformatics":[233],"online.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2019-01-25T00:00:00"}