Mammalian Genome

, Volume 19, Issue 10, pp 687–690

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. Beier
Article

DOI: 10.1007/s00335-008-9149-2

Cite this article as:
Beckstead, W.A., Bjork, B.C., Stottmann, R.W. et al. Mamm Genome (2008) 19: 687. doi:10.1007/s00335-008-9149-2

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/.

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
  1. 1.Department of BiologyBrigham Young UniversityProvoUSA
  2. 2.Bioinformatics Graduate ProgramBoston UniversityBostonUSA
  3. 3.Genetics Division, Brigham and Women’s HospitalHarvard Medical SchoolBostonUSA