{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T02:55:38Z","timestamp":1775271338026,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,8]],"date-time":"2019-05-08T00:00:00Z","timestamp":1557273600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1603120"],"award-info":[{"award-number":["U1603120"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31571314"],"award-info":[{"award-number":["31571314"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771394"],"award-info":[{"award-number":["31771394"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Foundation of iGeneTech","award":["2016SX001"],"award-info":[{"award-number":["2016SX001"]}]},{"name":"Research Foundation of iGeneTech","award":["2017SX003"],"award-info":[{"award-number":["2017SX003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Quality control (QC) for lab-designed primers is crucial for the success of a polymerase chain reaction (PCR). Here, we present MFEprimer-3.0, a functional primer quality control program for checking non-specific amplicons, dimers, hairpins and other parameters. The new features of the current version include: (i) more sensitive binding site search using the updated k-mer algorithm that allows mismatches within the k-mer, except for the first base at the 3\u2032 end. The binding sites of each primer with a stable 3\u2032 end are listed in the output; (ii) new algorithms for rapidly identifying self-dimers, cross-dimers and hairpins; (iii) the command-line version, which has an added option of JSON output to enhance the versatility of MFEprimer by acting as a QC step in the \u2018primer design \u2192 quality control \u2192 redesign\u2019 pipeline; (iv) a function for checking whether the binding sites contain single nucleotide polymorphisms (SNPs), which will affect the consistency of binding efficiency among different samples. In summary, MFEprimer-3.0 is updated with the well-tested PCR primer QC program and it can be integrated into various PCR primer design applications as a QC module. The MFEprimer-3.0 server is freely accessible without any login requirement at: https:\/\/mfeprimer3.igenetech.com\/ and https:\/\/www.mfeprimer.com\/. The source code for the command-line version is available upon request.<\/jats:p>","DOI":"10.1093\/nar\/gkz351","type":"journal-article","created":{"date-parts":[[2019,4,25]],"date-time":"2019-04-25T15:20:13Z","timestamp":1556205613000},"page":"W610-W613","source":"Crossref","is-referenced-by-count":90,"title":["MFEprimer-3.0: quality control for PCR primers"],"prefix":"10.1093","volume":"47","author":[{"given":"Kun","family":"Wang","sequence":"first","affiliation":[{"name":"Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, China"},{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Haiwei","family":"Li","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Yue","family":"Xu","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Qianzhi","family":"Shao","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Jianming","family":"Yi","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Ruichao","family":"Wang","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Wanshi","family":"Cai","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Xingyi","family":"Hang","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]},{"given":"Chenggang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Radiation Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100850, China"}]},{"given":"Haoyang","family":"Cai","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, China"}]},{"given":"Wubin","family":"Qu","sequence":"additional","affiliation":[{"name":"iGeneTech Bioscience Co., Ltd, Beijing 102206, China"}]}],"member":"286","published-online":{"date-parts":[[2019,5,8]]},"reference":[{"key":"2019062808125972500_B1","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1186\/1471-2105-11-143","article-title":"MPprimer: a program for reliable multiplex PCR primer design","volume":"11","author":"Shen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2019062808125972500_B2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1007\/978-1-4939-7142-8_6","article-title":"Design and application of multiplex PCR Seq for the detection of somatic mutations associated with myeloid malignancies","volume":"1633","author":"Park","year":"2017","journal-title":"Methods Mol. 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