PolyMarker

PolyMarker web portal is a pipeline for the development of single nucleotide polymorphism (SNP) assays. The PolyMarker algorithm generates KASP assays based on a three primer system and uses multiple sequence alignment of a target SNP sequence and a reference genome sequence to compute informative polymorphic positions of the homoeologs; genome-specific, varietal polymorphism, homoeologous, and genome semi-specific. In addition, PolyMarker site includes a REST API for remote access.

Topic

DNA polymorphism;Probes and primers

Detail

  • Operation: Primer and probe design

  • Software interface: Command-line user interface;Web service

  • Language: Ruby

  • License: Not stated

  • Cost: Free

  • Version name: -

  • Credit: UK Biotechnology and Biological Sciences Research Council (BBSRC, Norwich Research Park PhD Studentship, The Genome Analysis Centre Funding.

  • Input: -

  • Output: -

  • Contact: Ricardo.Ramirez-Gonzalez@tgac.ac.uk

  • Collection: -

  • Maturity: Mature

Publications

  • RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.
  • Ramirez-Gonzalez RH, Segovia V, Bird N, Fenwick P, Holdgate S, Berry S, Jack P, Caccamo M, Uauy C. RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol J. 2015 Jun;13(5):613-24. doi: 10.1111/pbi.12281. Epub 2014 Nov 8. PMID: 25382230.
  • https://doi.org/10.1111/pbi.12281
  • PMID: 25382230
  • PMC: -

Download and documentation

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