Scripts for design of PCR-based Marker Assays from DNA sequence variant data and optimised design of high-resolution melting PCR assays using the uMelt web service provided by the Wittwer Lab at University of Utah https://www.dna.utah.edu/umelt/umelt.html
Xml wrappers are included for use in the Galaxy workflow environment. Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/ hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers. (These are now (2015) quite old and we plan to replace these with containerized verisons using Docker.)
The primer design tool design_primers.py now uses the excellent primer3-py See http://benpruitt.github.io/primer3-py/index.html
- Linux or OSX - not tested on Windows (use Docker or VM)
- Python 2.7
- BioPython see https://pypi.python.org/pypi/biopython
- BcBio-gff
- Primer3-py
pip install bcbio-gff primer3-py
N.B. Primer3 install is NOT required now since design is handled by primer3-py
CITATION A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: Application For Development Of A Framework Linkage Map In Bulb Onion (Allium cepa L.) (2012)
Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
BMC Genomics 2012, 13:637 http://www.biomedcentral.com/1471-2164/13/637/abstract
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Zachary Dwight1, Robert Palais and Carl T. Wittwer http://bioinformatics.oxfordjournals.org/content/27/7/1019
Acknowledgements Development of these tools was funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG) See http://www.visg.co.nz