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Nucleic Acids Research 2005 33(Web Server Issue):W544-W547; doi:10.1093/nar/gki377
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

MuPlex: multi-objective multiplex PCR assay design

John Rachlin1,*, Chunming Ding2, Charles Cantor1,3,4,6 and Simon Kasif1,3,5

1Bioinformatics Program, Boston University Boston, MA 02215, USA 2Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories, Hong Kong Special Administrative Region, China 3Department of Biomedical Engineering, Boston University Boston, MA 02215, USA 4Center for Advanced Biotechnology, Boston University Boston, MA 02215, USA 5Center for Advanced Genomic Technologies, Boston University Boston, MA 02215, USA 6SEQUENOM, Inc. San Diego, CA 92121-1331, USA

*To whom correspondence should be addressed. Tel: +1 617 921 9669; Fax: +1 617 353 4814; Email: rachlin{at}bu.edu

Received February 14, 2005. Revised March 8, 2005. Accepted March 8, 2005.

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.


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