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.
%0 Journal Article
%1 rachlin_muplex:_2005
%A Rachlin, John
%A Ding, Chunming
%A Cantor, Charles
%A Kasif, Simon
%D 2005
%J Nucleic Acids Research
%K Algorithms, Analysis, Chain Humans, Interface Internet, Nucleotide, Polymerase Polymorphism, Primers, Reaction, Sequence Single Software, {DNA,} {DNA} {User-Computer}
%N Web Server issue
%P W544--7
%R 10.1093/nar/gki377
%T MuPlex: multi-objective multiplex PCR assay design
%U http://www.ncbi.nlm.nih.gov/pubmed/15980531
%V 33
%X 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.
@article{rachlin_muplex:_2005,
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.}},
added-at = {2011-03-11T10:05:34.000+0100},
author = {Rachlin, John and Ding, Chunming and Cantor, Charles and Kasif, Simon},
biburl = {https://www.bibsonomy.org/bibtex/21f7138cd805861d67897bec719e829e4/jelias},
doi = {10.1093/nar/gki377},
interhash = {0d15117ede5353b4fde53c53fef72f62},
intrahash = {1f7138cd805861d67897bec719e829e4},
issn = {1362-4962},
journal = {Nucleic Acids Research},
keywords = {Algorithms, Analysis, Chain Humans, Interface Internet, Nucleotide, Polymerase Polymorphism, Primers, Reaction, Sequence Single Software, {DNA,} {DNA} {User-Computer}},
month = jul,
note = {{PMID:} 15980531},
number = {Web Server issue},
pages = {W544--7},
shorttitle = {{MuPlex}},
timestamp = {2011-03-11T10:05:49.000+0100},
title = {{MuPlex:} multi-objective multiplex {PCR} assay design},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15980531},
volume = 33,
year = 2005
}