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MPD specifications

Information


Unique identifier OMICS_14711
Name MPD
Alternative name Multiplex Primer Design
Interface Web user interface
Restrictions to use None
Input data A list of coordinates to amplify
Input format BED
Output data The final primer design summary viewed in the browser
Programming languages Javascript, Perl
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Documentation


Maintainer


  • person_outline Thomas Wingo

Additional information


A registration is needed to access to tools.

Information


Unique identifier OMICS_14711
Name MPD
Alternative name Multiplex Primer Design
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of coordinates to amplify
Input format BED
Output data The final primer design summary
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL https://codeload.github.com/wingolab-org/mpd-c/legacy.tar.gz/master
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Thomas Wingo

Additional information


A registration is needed to access to tools.

Publication for Multiplex Primer Design

MPD citations

 (4)
call_split

Updated Campylobacter jejuni Capsule PCR Multiplex Typing System and Its Application to Clinical Isolates from South and Southeast Asia

2015
PLoS One
PMCID: 4668122
PMID: 26630669
DOI: 10.1371/journal.pone.0144349
call_split See protocol

[…] a local stand alone BLAST using a database encompassing the nucleotides sequences of all 47 available C. jejuni capsule loci (C. T. Parker, unpublished). The selected nucleotide regions were used for multiplex primer design. The sites where the primers were designed are displayed in . Multiplex primers were designed via the online software Primer3 [] using the following parameters: length between […]

library_books

Methods for Multiplex Template Sampling in Digital PCR Assays

2014
PLoS One
PMCID: 4031183
PMID: 24854517
DOI: 10.1371/journal.pone.0098341

[…] nable. The downside of modular type of primers is their higher synthesis and purification cost. Although not tested here, we believe these multiplexing methods can be further improved by implementing multiplex primer design strategies that minimize interactions . In addition we show that in some cases multiplexing can be effectively resolved by using primer pairs that each target more than one chr […]

library_books

Multiplex primer prediction software for divergent targets

2009
Nucleic Acids Res
PMCID: 2770652
PMID: 19759213
DOI: 10.1093/nar/gkp659

[…] he for viral identification when singleplex PCR has failed or there are a few dozen likely candidates but the expense of metagenomic sequencing or high-density microarrays is unwarranted (). However, multiplex primer design for many highly divergent targets is challenging since no universally conserved primers may exist, and finding sets of primers likely to function well in multiplex (e.g. isothe […]

library_books

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments

2006
Nucleic Acids Res
PMCID: 1747188
PMID: 17135211
DOI: 10.1093/nar/gkl966

[…] s, melting temperature and maximum homopolymeric runs for primers (). Based on these considerations, many software tools have been written for the design of non-degenerate primers (–). Degenerate and multiplex primer design has been classified as an optimization problem (). Thus, heuristic algorithms have been particularly useful in addressing the challenge. Examples include the methods of Doi and […]

Citations

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MPD institution(s)
Division of Neurology, Atlanta VA Medical Center, Decatur, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
MPD funding source(s)
Supported by the Veterans Health Administration (BX001820), National Institutes of Health (AG025688), and the Emory Integrated Genomics Core (EIGC).

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