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

PolyMarker: A fast polyploid primer design pipeline.

Author information

1
The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK and National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK.
2
The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK and National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK and National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK.

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.

PMID:
25649618
PMCID:
PMC4765872
DOI:
10.1093/bioinformatics/btv069
[Indexed for MEDLINE]
Free PMC Article

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