Charles Cantor

MuPlex: multi-objective multiplex PCR assay design

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 .

The MuPlex homepage

Copyright information: Taken from MuPlex: multi-objective multiplex PCR assay designNucleic Acids Research 2005;33(Web Server issue):W544-W547.Published online 27 Jun 2005PMCID:PMC1160138.© The Author 2005. Published by Oxford University Press. All rights reserved Users specify primer selection criteria and provide a collection of SNPs in the FASTA format. The system emails to the user one or more solution alternatives revealing key design tradeoffs.