PolyMarker: A fast polyploid primer design pipeline.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 25649618.
- Also identified by DOI 10.1093/bioinformatics/btv069 and PMC identifier 4765872.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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. PolyMarker is available as a ruby BioGem: bio-polyploid-tools. Web interface: http://polymarker.tgac.ac.uk.
Medical subject headings
- DNA Primers
- Genetic Markers
- Polymorphism, Single Nucleotide
- Polyploidy
- Sequence Analysis, DNA
- Software
- Triticum