{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T18:40:01Z","timestamp":1766428801666,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T00:00:00Z","timestamp":1546905600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Grain Legume and Dryland Cereals"},{"name":"GLDC"},{"name":"Grain Research and Development Cooperation"},{"DOI":"10.13039\/501100000980","name":"GRDC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000980","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in\u00a0vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes\/SNPs\/simple sequence repeats and those that are shared between in\u00a0vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in\u00a0vitro results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code available under GNU GPL at (http:\/\/www.ageri.sci.eg\/index.php\/facilities-services\/ageri-softwares\/kaspspoon).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz004","type":"journal-article","created":{"date-parts":[[2019,1,4]],"date-time":"2019-01-04T20:11:19Z","timestamp":1546632679000},"page":"3187-3190","source":"Crossref","is-referenced-by-count":16,"title":["KASPspoon: an <i>in\u00a0vitro<\/i> and <i>in silico<\/i> PCR analysis tool for high-throughput SNP genotyping"],"prefix":"10.1093","volume":"35","author":[{"given":"Alsamman M","family":"Alsamman","sequence":"first","affiliation":[{"name":"Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt"}]},{"given":"Shafik D","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute Department of Genome Mapping, Molecular Genetics and , Giza, Egypt"}]},{"given":"Aladdin","family":"Hamwieh","sequence":"additional","affiliation":[{"name":"International Center for Agricultural Research in the Dry Areas (ICARDA) Department of Biotechnology, , Cairo, Egypt"}]}],"member":"286","published-online":{"date-parts":[[2019,1,8]]},"reference":[{"key":"2023062711311832300_btz004-B1","doi-asserted-by":"crossref","DOI":"10.1007\/3-540-56024-6_15","article-title":"Fast and practical approximate string matching","volume-title":"Combinatorial Pattern Matching. 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