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MuPlex: Multi-Objective Multiplex PCR Assay Design

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dc.contributor.author Rachlin, John en_US
dc.contributor.author Ding, Chunming en_US
dc.contributor.author Cantor, Charles en_US
dc.contributor.author Kasif, Simon en_US
dc.date.accessioned 2012-01-11T00:39:15Z
dc.date.available 2012-01-11T00:39:15Z
dc.date.issued 2005-06-27 en_US
dc.identifier.citation Rachlin, John, Chunming Ding, Charles Cantor, Simon Kasif. "MuPlex: multi-objective multiplex PCR assay design" Nucleic Acids Research 33(Web Server issue): W544-W547. (2005) en_US
dc.identifier.issn 1362-4962 en_US
dc.identifier.uri http://hdl.handle.net/2144/3023
dc.description.abstract We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious microorganisms, whole-genome sequencing and closure, forensic analysis and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays is computationally challenging because it involves tradeoffs among competing objectives, and extensive computational analysis is required in order to screen out primer-pair cross interactions. With MuPlex, users specify a set of DNA sequences along with primer selection criteria, interaction parameters and the target multiplexing level. MuPlex designs a set of multiplex PCR assays designed to cover as many of the input sequences as possible. MuPlex provides multiple solution alternatives that reveal tradeoffs among competing objectives. MuPlex is uniquely designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage of potentially thousands of single nucleotide polymorphisms is required. The server is available at http://genomics14.bu.edu:8080/MuPlex/MuPlex.html. en_US
dc.description.sponsorship National Science Foundation (DBI-0239435, ITR-048715); National Human Genome Research Institute (1R33HG002850-01A1) en_US
dc.language.iso en en_US
dc.publisher Oxford University Press en_US
dc.title MuPlex: Multi-Objective Multiplex PCR Assay Design en_US
dc.type article en_US
dc.identifier.doi 10.1093/nar/gki377 en_US
dc.identifier.pubmedid 15980531 en_US
dc.identifier.pmcid 1160138 en_US


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