{"id":"https://openalex.org/W2908992500","doi":"https://doi.org/10.1101/522045","title":"KASP-Hedgehog: Efficient and routine tool for allele specific primer design using multidisciplinary data types","display_name":"KASP-Hedgehog: Efficient and routine tool for allele specific primer design using multidisciplinary data types","publication_year":2019,"publication_date":"2019-01-16","ids":{"openalex":"https://openalex.org/W2908992500","doi":"https://doi.org/10.1101/522045","mag":"2908992500"},"language":"en","primary_location":{"id":"doi:10.1101/522045","doi":"https://doi.org/10.1101/522045","is_oa":true,"landing_page_url":"https://doi.org/10.1101/522045","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/16/522045.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/16/522045.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083340569","display_name":"Alsamman M. Alsamman","orcid":"https://orcid.org/0000-0002-7765-5035","observed_orcids":["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":false,"raw_author_name":"M.A Alsamman","raw_affiliation_strings":["Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","Agricultural Genetic Engineering Research Institute, PO Box269, Giza, Egypt"],"raw_orcid":"https://orcid.org/0000-0002-7765-5035","affiliations":[{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]},{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box269, Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033120710","display_name":"Mohamed Abdelsattar","orcid":"https://orcid.org/0000-0003-0851-8309","observed_orcids":["https://orcid.org/0000-0003-0851-8309"]},"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":"M Abdelsattar","raw_affiliation_strings":["Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","Agricultural Genetic Engineering Research Institute, PO Box269, Giza, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]},{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box269, 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","observed_orcids":["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":"S.D. Ibrahim","raw_affiliation_strings":["Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","Agricultural Genetic Engineering Research Institute, PO Box269, Giza, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box12619, Giza, Egypt","institution_ids":["https://openalex.org/I4210129354"]},{"raw_affiliation_string":"Agricultural Genetic Engineering Research Institute, PO Box269, 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","observed_orcids":["https://orcid.org/0000-0001-6060-5560"]},"institutions":[{"id":"https://openalex.org/I192358263","display_name":"International Center for Agricultural Research in the Dry Areas","ror":"https://ror.org/02n2syw04","country_code":"LB","type":"facility","lineage":["https://openalex.org/I1286583668","https://openalex.org/I192358263"]}],"countries":["LB"],"is_corresponding":false,"raw_author_name":"Hamwieh Aladdin","raw_affiliation_strings":["International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 2416, Cairo, Egypt","International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 416, Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 2416, Cairo, Egypt","institution_ids":["https://openalex.org/I192358263"]},{"raw_affiliation_string":"International Center for Agricultural Research in the Dry Areas (ICARDA), PO Box 416, Cairo, Egypt","institution_ids":["https://openalex.org/I192358263"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"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":0.33059999346733093,"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":0.33059999346733093,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.32519999146461487,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.16920000314712524,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/kasp-genotyping","display_name":"KASP genotyping","score":0.7820000052452087},{"id":"https://openalex.org/keywords/snp-selection","display_name":"SNP selection","score":0.5720000267028809},{"id":"https://openalex.org/keywords/degenerate-primers","display_name":"degenerate primers","score":0.8240000009536743},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.5950000286102295},{"id":"https://openalex.org/keywords/snp-database","display_name":"SNP database","score":0.49000000953674316},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"graphical user interface","score":0.6140000224113464},{"id":"https://openalex.org/keywords/bioinformatics-software","display_name":"bioinformatics software","score":0.6539999842643738}],"concepts":[{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.5704944133758545},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5613411664962769},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.5411900281906128},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.47308236360549927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4536031484603882},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.429293155670166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3785528838634491},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.35650837421417236},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.13740411400794983},{"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":[],"locations_count":1,"locations":[{"id":"doi:10.1101/522045","doi":"https://doi.org/10.1101/522045","is_oa":true,"landing_page_url":"https://doi.org/10.1101/522045","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/16/522045.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/522045","doi":"https://doi.org/10.1101/522045","is_oa":true,"landing_page_url":"https://doi.org/10.1101/522045","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/01/16/522045.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2908992500.pdf","grobid_xml":"https://content.openalex.org/works/W2908992500.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1926675790","https://openalex.org/W1971403296","https://openalex.org/W1973408460","https://openalex.org/W2033409266","https://openalex.org/W2130660012","https://openalex.org/W2132926880","https://openalex.org/W2145928478","https://openalex.org/W2156256232","https://openalex.org/W2162098634","https://openalex.org/W2399909957","https://openalex.org/W2762981192","https://openalex.org/W2802953232","https://openalex.org/W2950065786"],"related_works":["https://openalex.org/W4417501294","https://openalex.org/W2130660012","https://openalex.org/W4214670042","https://openalex.org/W4366083153","https://openalex.org/W2105086662","https://openalex.org/W2982199258","https://openalex.org/W2096760544","https://openalex.org/W2120515593","https://openalex.org/W4409451837","https://openalex.org/W601414050"],"abstract_inverted_index":{"Abstract":[0],"The":[1],"Integration":[2],"of":[3,21,71],"known":[4],"nucleotide":[5,82],"variations":[6,83],"in":[7,110,125,136,157,166],"breeding":[8],"programs":[9],"and":[10,18,36,51,84,117,142,151],"medical":[11],"assessments":[12],"demands":[13],"the":[14,62],"ability":[15,63],"to":[16,64,103,112,138,159],"scan":[17],"validate":[19],"thousands":[20],"gene-affected":[22],"SNPs.":[23],"Designing":[24],"PCR":[25,56,114,127],"primers":[26,38,106,131,140],"targeting":[27],"these":[28],"SNPs":[29,76,86,101],"require":[30],"computational":[31],"tools":[32],"could":[33,163],"generate":[34],"accurate":[35],"target-specific":[37],"using":[39],"multidisciplinary":[40],"data":[41],"types":[42],"with":[43,80,87,107],"high":[44],"accuracy.":[45],"KASP-Hedgehog":[46,59],"is":[47],"a":[48,69,160],"local-installation,":[49],"simple":[50],"routine":[52],"tool":[53,95],"for":[54,77,129],"allele-specific":[55,105],"primer":[57,67],"design.":[58],"gives":[60],"user":[61,144,154],"design":[65],"KASP":[66],"from":[68],"variety":[70],"genomic":[72,78],"data,":[73],"extract":[74],"bi-allelic":[75],"sequences":[79,135],"unknown":[81],"select":[85],"potential":[88],"effect":[89],"depending":[90],"on":[91],"gene":[92],"annotation.":[93],"This":[94],"can":[96],"use":[97],"user-provided":[98],"or":[99],"self-produced":[100],"database":[102],"create":[104],"degenerate":[108],"structure":[109],"order":[111,137],"enhance":[113],"assay":[115],"selectivity":[116,141],"increase":[118,139],"amplification":[119],"reaction.":[120],"Additionally,":[121],"it":[122,148],"run":[123],"an":[124],"silico":[126],"test":[128],"designed":[130],"against":[132],"provided":[133],"FASTA":[134],"provide":[143],"more":[145],"information.":[146],"Moreover,":[147],"has":[149],"interactive":[150],"user-friendly":[152],"graphical":[153],"interface":[155],"(GUI)":[156],"addition":[158],"command-line":[161],"package":[162],"be":[164],"integrated":[165],"different":[167],"bioinformatics":[168],"pipelines.":[169]},"counts_by_year":[{"year":2020,"cited_by_count":2}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2019-01-25T00:00:00"}
