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Mamm Genome. 2008 Oct-Dec;19(10-12):687-90. doi: 10.1007/s00335-008-9149-2. Epub 2008 Oct 29.

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

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

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/ .

PMID:
18958524
[PubMed - indexed for MEDLINE]
PMCID:
PMC3001109
Free PMC Article

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