{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T23:32:52Z","timestamp":1780443172347,"version":"3.54.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We developed a program named MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3 \u2032 -end of the primer, melting temperature, GC content and number of binding sites between the primer and DNA templates. MFEprimer can help the user to select more suitable primers before running either standard or multiplex PCR reactions. The cDNA and genomic DNA databases of 10 widely used species, as well as user custom databases, were used as DNA templates for analyzing primers specificity. Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking.<\/jats:p>\n               <jats:p>Availability: The web service of MFEprimer is freely available at http:\/\/biocompute.bmi.ac.cn\/MFEprimer\/. A stand-alone version of MFEprimer can be downloaded at http:\/\/biocompute.bmi.ac.cn\/MFEprimer\/download\/. Primer3Plus on our server is located at http:\/\/biocompute.bmi.ac.cn\/MFEprimer\/primer3plus.cgi. All programs are licensed under the General Public License (Free Software Foundation, 1991).<\/jats:p>\n               <jats:p>Contact: \u00a0zhangcg@bmi.ac.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn614","type":"journal-article","created":{"date-parts":[[2008,11,28]],"date-time":"2008-11-28T01:24:25Z","timestamp":1227835465000},"page":"276-278","source":"Crossref","is-referenced-by-count":52,"title":["MFEprimer: multiple factor evaluation of the specificity of PCR primers"],"prefix":"10.1093","volume":"25","author":[{"given":"Wubin","family":"Qu","sequence":"first","affiliation":[{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"},{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyong","family":"Shen","sequence":"additional","affiliation":[{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongsheng","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Yang","sequence":"additional","affiliation":[{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenggang","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,11,27]]},"reference":[{"key":"2023013109593897700_B1","doi-asserted-by":"crossref","first-page":"10581","DOI":"10.1021\/bi962590c","article-title":"Thermodynamics and NMR of internal GT mismatches in DNA","volume":"36","author":"Allawi","year":"1997","journal-title":"Biochemistry"},{"key":"2023013109593897700_B2","doi-asserted-by":"crossref","first-page":"9435","DOI":"10.1021\/bi9803729","article-title":"Nearest-neighbor thermodynamics of internal A center dot C mismatches in DNA: sequence dependence and pH effects","volume":"37","author":"Allawi","year":"1998","journal-title":"Biochemistry"},{"key":"2023013109593897700_B3","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.1021\/bi9724873","article-title":"Nearest neighbor thermodynamic parameters for internal G center dot A mismatches in DNA","volume":"37","author":"Allawi","year":"1998","journal-title":"Biochemistry"},{"key":"2023013109593897700_B4","doi-asserted-by":"crossref","first-page":"2694","DOI":"10.1093\/nar\/26.11.2694","article-title":"Thermodynamics of internal C center dot T mismatches in DNA","volume":"26","author":"Allawi","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2023013109593897700_B5","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023013109593897700_B6","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/978-1-59745-528-2_10","article-title":"Fast masking of repeated primer binding sites in eukaryotic genomes","volume":"402","author":"Andreson","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"2023013109593897700_B7","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 Res"},{"key":"2023013109593897700_B8","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1093\/bioinformatics\/bth257","article-title":"PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design","volume":"20","author":"Boutros","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B9","doi-asserted-by":"crossref","first-page":"3918","DOI":"10.1093\/bioinformatics\/bti633","article-title":"Oligonucleotide properties determination and primer designing: a critical examination of predictions","volume":"21","author":"Chavali","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B10","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1186\/1471-2105-7-179","article-title":"AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs","volume":"7","author":"Han","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013109593897700_B11","first-page":"656","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023013109593897700_B12","doi-asserted-by":"crossref","first-page":"4335","DOI":"10.1093\/nar\/gki739","article-title":"miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST","volume":"33","author":"Kim","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013109593897700_B13","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1093\/bioinformatics\/16.11.1052","article-title":"MPBLAST: improved BLAST performance with multiplexed queries","volume":"16","author":"Korf","year":"2000","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B14","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1093\/bioinformatics\/17.2.192","article-title":"Virtual PCR","volume":"17","author":"Lexa","year":"2001","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B15","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1093\/bioinformatics\/btg350","article-title":"PRIMEX: rapid identification of oligonucleotide matches in whole genomes","volume":"19","author":"Lexa","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B16","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1093\/bioinformatics\/bth254","article-title":"PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR","volume":"20","author":"Marshall","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B17","doi-asserted-by":"crossref","first-page":"4363","DOI":"10.1093\/bioinformatics\/bti716","article-title":"A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3\u2032-end subsequences","volume":"21","author":"Miura","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013109593897700_B18","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.mcp.2004.05.007","article-title":"Selection for 3\u2032 end triplets for polymerase chain reaction primers","volume":"18","author":"Onodera","year":"2004","journal-title":"Mol. Cell. Probes"},{"key":"2023013109593897700_B19","doi-asserted-by":"crossref","first-page":"3468","DOI":"10.1021\/bi9825091","article-title":"Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A center dot A, C center dot C, G center dot G, and T center dot T mismatches","volume":"38","author":"Peyret","year":"1999","journal-title":"Biochemistry"},{"key":"2023013109593897700_B20","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume":"132","author":"Rozen","year":"2000","journal-title":"Methods Mol. Biol."},{"key":"2023013109593897700_B21","first-page":"88","article-title":"Priming efficiency in PCR","volume":"86","author":"Rychlik","year":"1995","journal-title":"Biotechniques"},{"key":"2023013109593897700_B22","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics","volume":"95","author":"SantaLucia","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013109593897700_B23","doi-asserted-by":"crossref","first-page":"6749","DOI":"10.1093\/nar\/17.16.6749","article-title":"Minimal homology requirements for PCR primers","volume":"17","author":"Sommer","year":"1989","journal-title":"Nucleic Acids Res."},{"key":"2023013109593897700_B24","doi-asserted-by":"crossref","first-page":"W71","DOI":"10.1093\/nar\/gkm306","article-title":"Primer3Plus, an enhanced web interface to Primer3","volume":"35","author":"Untergasser","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013109593897700_B25","doi-asserted-by":"crossref","first-page":"1956","DOI":"10.1093\/clinchem\/47.11.1956","article-title":"Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas","volume":"47","author":"von Ahsen","year":"2001","journal-title":"Clin. Chem."},{"key":"2023013109593897700_B26","doi-asserted-by":"crossref","first-page":"e154","DOI":"10.1093\/nar\/gng154","article-title":"A PCR primer bank for quantitative gene expression analysis","volume":"31","author":"Wang","year":"2003","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/2\/276\/48982158\/bioinformatics_25_2_276.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/2\/276\/48982158\/bioinformatics_25_2_276.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:36:57Z","timestamp":1675190217000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/2\/276\/220641"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,11,27]]},"references-count":26,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2009,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn614","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,1,15]]},"published":{"date-parts":[[2008,11,27]]}}}