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SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs

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Abstract

Genome-wide analysis of single nucleotide polymorphism (SNP) markers is an extremely efficient means for genetic mapping of mutations or traits in mice. However, this approach often defines a relatively large recombinant interval. To facilitate the refinement of this interval, we developed the program SNP2RFLP. This program can be used to identify region-specific SNPs in which the polymorphic nucleotide creates a restriction fragment length polymorphism (RFLP) that can be readily assayed at the benchtop using restriction enzyme digestion of SNP-containing PCR products. The program permits user-defined queries that maximize the informative markers for a particular application. This facilitates fine-mapping in a region containing a mutation of interest, which should prove valuable to the mouse genetics community. SNP2RFLP and further details are publicly available at http://genetics.bwh.harvard.edu/snp2rflp/.

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Author notes

  1. Wesley A. Beckstead

    Present address: Bioinformatics Graduate Program, Boston University, Boston, MA, 02215, USA

Authors and Affiliations

  1. Department of Biology, Brigham Young University, Provo, UT, 84602, USA

    Wesley A. Beckstead

  2. Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA

    Bryan C. Bjork, Rolf W. Stottmann, Shamil Sunyaev & David R. Beier

Authors
  1. Wesley A. Beckstead
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  2. Bryan C. Bjork
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  3. Rolf W. Stottmann
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  4. Shamil Sunyaev
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  5. David R. Beier
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Corresponding author

Correspondence to David R. Beier.

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Beckstead, W.A., Bjork, B.C., Stottmann, R.W. et al. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs. Mamm Genome 19, 687–690 (2008). https://doi.org/10.1007/s00335-008-9149-2

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  • DOI: https://doi.org/10.1007/s00335-008-9149-2

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