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. 2015 Jun 15;31(12):2038-9.
doi: 10.1093/bioinformatics/btv069. Epub 2015 Feb 2.

PolyMarker: A fast polyploid primer design pipeline

Ricardo H Ramirez-Gonzalez  1 , Cristobal Uauy  2 , Mario Caccamo  1
Affiliations

PolyMarker: A fast polyploid primer design pipeline

Ricardo H Ramirez-Gonzalez et al. Bioinformatics. .

Abstract

The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specific. PolyMarker is a pipeline that generates SNP markers by selecting candidate primers for a specified genome using local alignments and standard primer design tools to test the viability of the primers. A command line tool and a web interface are available to the community.

Availability and implementation: PolyMarker is available as a ruby BioGem: bio-polyploid-tools. Web interface: http://polymarker.tgac.ac.uk.

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Figures

Fig. 1.
Fig. 1.
Implementation of PolyMarker. External programs are in squares, trapezoids represent the intermediate files and the document symbols represent inputs and outputs
See this image and copyright information in PMC

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