{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T12:51:27Z","timestamp":1776343887539,"version":"3.51.2"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,19]],"date-time":"2018-01-19T00:00:00Z","timestamp":1516320000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The standalone version of primer3_masker is implemented in C. The source code is freely available at https:\/\/github.com\/bioinfo-ut\/primer3_masker\/ (standalone version for Linux and macOS) and at https:\/\/github.com\/primer3-org\/primer3\/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http:\/\/primer3.ut.ee\/.<\/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\/bty036","type":"journal-article","created":{"date-parts":[[2018,1,18]],"date-time":"2018-01-18T20:27:50Z","timestamp":1516307270000},"page":"1937-1938","source":"Crossref","is-referenced-by-count":484,"title":["Primer3_masker: integrating masking of template sequence with primer design software"],"prefix":"10.1093","volume":"34","author":[{"given":"Triinu","family":"K\u00f5ressaar","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]},{"given":"Maarja","family":"Lepamets","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]},{"given":"Lauris","family":"Kaplinski","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]},{"given":"Kairi","family":"Raime","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]},{"given":"Reidar","family":"Andreson","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]},{"given":"Maido","family":"Remm","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia"}]}],"member":"286","published-online":{"date-parts":[[2018,1,19]]},"reference":[{"key":"2023012713554731700_bty036-B1","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/1471-2105-7-172","article-title":"GENOMEMASKER package for designing unique genomic PCR primers","volume":"7","author":"Andreson","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012713554731700_bty036-B2","doi-asserted-by":"crossref","first-page":"W651","DOI":"10.1093\/nar\/gkl125","article-title":"SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes","volume":"34","author":"Andreson","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023012713554731700_bty036-B3","doi-asserted-by":"crossref","first-page":"e66.","DOI":"10.1093\/nar\/gkn290","article-title":"Predicting failure rate of PCR in large genomes","volume":"36","author":"Andreson","year":"2008","journal-title":"Nucleic Acids 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