SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs.
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/ .
Beckstead
Wesley A
WA
Department of Biology, Brigham Young University, Provo, UT 84602, USA.
Bjork
Bryan C
BC
Stottmann
Rolf W
RW
Sunyaev
Shamil
S
Beier
David R
DR
D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D051379:Mice; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface