Mammalian Genome

, Volume 19, Issue 10–12, pp 687–690 | Cite as

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

  • Wesley A. Beckstead
  • Bryan C. Bjork
  • Rolf W. Stottmann
  • Shamil Sunyaev
  • David R. BeierEmail author


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


Single Nucleotide Polymorphism Restriction Fragment Length Polymorphism Single Nucleotide Polymorphism Marker Informative Marker Single Nucleotide Polymorphism Genotype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Wesley A. Beckstead
    • 1
    • 2
  • Bryan C. Bjork
    • 3
  • Rolf W. Stottmann
    • 3
  • Shamil Sunyaev
    • 3
  • David R. Beier
    • 3
    Email author
  1. 1.Department of BiologyBrigham Young UniversityProvoUSA
  2. 2.Bioinformatics Graduate ProgramBoston UniversityBostonUSA
  3. 3.Genetics Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonUSA

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