{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:48:19Z","timestamp":1761662899084},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2189,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The development of new high-throughput genotyping products requires a significant investment in testing and training samples to evaluate and optimize the product before it can be used reliably on new samples. One reason for this is current methods for automated calling of genotypes are based on clustering approaches which require a large number of samples to be analyzed simultaneously, or an extensive training dataset to seed clusters. In systems where inbred samples are of primary interest, current clustering approaches perform poorly due to the inability to clearly identify a heterozygote cluster.<\/jats:p>\n               <jats:p>Results: As part of the development of two custom single nucleotide polymorphism genotyping products for Oryza sativa (domestic rice), we have developed a new genotype calling algorithm called \u2018ALCHEMY\u2019 based on statistical modeling of the raw intensity data rather than modelless clustering. A novel feature of the model is the ability to estimate and incorporate inbreeding information on a per sample basis allowing accurate genotyping of both inbred and heterozygous samples even when analyzed simultaneously. Since clustering is not used explicitly, ALCHEMY performs well on small sample sizes with accuracy exceeding 99% with as few as 18 samples.<\/jats:p>\n               <jats:p>Availability: ALCHEMY is available for both commercial and academic use free of charge and distributed under the GNU General Public License at http:\/\/alchemy.sourceforge.net\/<\/jats:p>\n               <jats:p>Contact: \u00a0mhw6@cornell.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq533","type":"journal-article","created":{"date-parts":[[2010,10,19]],"date-time":"2010-10-19T04:15:50Z","timestamp":1287461750000},"page":"2952-2960","source":"Crossref","is-referenced-by-count":45,"title":["ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations"],"prefix":"10.1093","volume":"26","author":[{"given":"Mark H.","family":"Wright","sequence":"first","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]},{"given":"Chih-Wei","family":"Tung","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]},{"given":"Keyan","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]},{"given":"Andy","family":"Reynolds","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]},{"given":"Susan R.","family":"McCouch","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]},{"given":"Carlos D.","family":"Bustamante","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, 102 Weill Hall and 2Department of Plant Breeding and Genetics, Emerson Hall, Cornell University, Ithaca, NY 14853, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,10,5]]},"reference":[{"key":"2023012507530436900_B1","author":"Affymetrix Inc.","year":"2006","journal-title":"BRLMM: an improved genotype calling method for the genechip\u00ae mapping 500k array set."},{"key":"2023012507530436900_B2","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1126\/science.1174276","article-title":"The genetic architecture of maize flowering time","volume":"325","author":"Buckler","year":"2009","journal-title":"Science"},{"key":"2023012507530436900_B3","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1093\/biostatistics\/kxl042","article-title":"Exploration, normalization, and genotype calls of high-density oligonucleotide snp array data","volume":"8","author":"Carvalho","year":"2007","journal-title":"Biostatistics"},{"key":"2023012507530436900_B4","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1101\/sqb.2003.68.69","article-title":"Highly parallel snp genotyping","volume":"68","author":"Fan","year":"2003","journal-title":"Cold Spring Harb. 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