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author ben-warren
date Mon, 07 Jul 2014 19:28:17 -0400
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1 galaxy-pcr-markers 1 galaxy-pcr-markers
2 ================== 2 ==================
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4 Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in Galaxy workflow environment 4 Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in the Galaxy workflow environment
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6 Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/ 6 Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/
7 hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers 7 hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers
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9 NOTE that the primer design tool *design_primers.py* relies on EMBOSS ePrimer3 which depends on Primer3 1.1.4. 9 NOTE that the primer design tool *design_primers.py* no longer relies on EMBOSS ePrimer3 (which depends on Primer3 1.1.4.)
10 The updated tool *design_HRM_primers.py* does not have this restriction and should work with Primer3 V2. 10 and should work with Primer3 V2.
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12 Please see development branch HRM for optimised design of high-resolution melting PCR assays using the uMelt web service at University of Utah. 12 This release adds 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
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15 **CITATION** 15 **CITATION**
16 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) 16 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)
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18 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum 18 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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20 BMC Genomics 2012, 13:637 http://www.biomedcentral.com/1471-2164/13/637/abstract 20 BMC Genomics 2012, 13:637 http://www.biomedcentral.com/1471-2164/13/637/abstract
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22 uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application.
23 Zachary Dwight1, Robert Palais and Carl T. Wittwer http://bioinformatics.oxfordjournals.org/content/27/7/1019
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22 **Acknowledgements** 25 **Acknowledgements**
23 Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG) 26 Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG)
24 See http://www.visg.co.nz 27 See http://www.visg.co.nz