{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T10:39:32Z","timestamp":1722767972523},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"Abstract<\/jats:title>\n Summary: PriSM is a set of algorithms designed to select and match degenerate primer pairs for the amplification of viral genomes. The design of panels of hundreds of primer pairs takes just hours using this program, compared with days using a manual approach. PriSM allows for rapid in silico optimization of primers for downstream applications such as sequencing. As a validation, PriSM was used to create an amplification primer panel for human immunodeficiency virus (HIV) Clade B.<\/jats:p>\n Availability: The program is freely available for use at: www.broadinstitute.org\/perl\/seq\/specialprojects\/primerDesign.cgi<\/jats:p>\n Contact: \u00a0nlennon@broadinstitute.org<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq624","type":"journal-article","created":{"date-parts":[[2010,11,11]],"date-time":"2010-11-11T01:18:02Z","timestamp":1289438282000},"page":"266-267","source":"Crossref","is-referenced-by-count":12,"title":["PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes"],"prefix":"10.1093","volume":"27","author":[{"given":"Qing","family":"Yu","sequence":"first","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]},{"given":"Elizabeth M.","family":"Ryan","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]},{"given":"Todd M.","family":"Allen","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]},{"given":"Bruce W.","family":"Birren","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]},{"given":"Matthew R.","family":"Henn","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]},{"given":"Niall J.","family":"Lennon","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT & Harvard, Cambridge, MA 02142 and 2Ragon Institute of MGH, MIT & Harvard, 149 13th Street Charlestown, MA 02129, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,11,9]]},"reference":[{"key":"2023012512180202700_B1","doi-asserted-by":"crossref","first-page":"9216","DOI":"10.1128\/JVI.01041-08","article-title":"Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute\/early HIV-1 infection","volume":"82","author":"Brumme","year":"2008","journal-title":"J. Virol."},{"key":"2023012512180202700_B2","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1093\/nar\/gki425","article-title":"PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs","volume":"33","author":"Fredslund","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012512180202700_B3","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1093\/bioinformatics\/bth121","article-title":"Amplicon: software for designing PCR primers on aligned DNA sequences","volume":"20","author":"Jarman","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012512180202700_B4","doi-asserted-by":"crossref","first-page":"3225","DOI":"10.1128\/jvi.66.5.3225-3229.1992","article-title":"Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution","volume":"66","author":"Martell","year":"1992","journal-title":"J. Virol."},{"key":"2023012512180202700_B5","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume-title":"Bioinformatics Methods and Protocols: Methods in Molecular Biology.","author":"Rozen","year":"2000"},{"key":"2023012512180202700_B6","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gkm383","article-title":"PrimerZ: streamlined primer design for promoters, exons and human SNPs","volume":"35","author":"Tsai","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/266\/48869483\/bioinformatics_27_2_266.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/266\/48869483\/bioinformatics_27_2_266.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:54:49Z","timestamp":1674658489000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/2\/266\/284697"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,9]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2011,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq624","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,1,15]]},"published":{"date-parts":[[2010,11,9]]}}}