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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.
This publication is provided for historical reference only and the information may be out of date.
Could you tell me the names and the number of the mouse strains for which dbSNP has data? How do I access this data?
There is no listing of SNPs across all mouse strains. You can search between strains, and you can get a listing of all the mouse SNPs in dbSNP by searching Entrez SNP or downloading the mouse data from the dbSNP FTP site. (01/15/08)
After narrowing the range of my search for SNPs that are polymorphic between the C57BL6/J and 129 sv/j strains of mice by typing 3[CHR]105351425:107237468 [CHRPOS] into EntrezSNP, How do I get Entrez SNP to show me SNPs that are polymorphic between C57BL6/J and 129 sv/j?
Enter the following into Entrez SNP:
"Mouse[orgn] AND true[gtype] AND 3[CHR] AND 105351425:107237468 [CHRPOS]"
(11/06:02/14)
I want to find SNPs in the 129 and Bl6 mouse strains that are the same as each other but differ from BALB/c using the Search Mouse SNP between strains tool. I stipulated that BALB/c was to differ from 129/Sv, 129X1/SVJ, 129X1/SV, C57BL/6, C57BL/6J, and Mus musculus C57BL/6J. This query returns extra SNPs that do not conform to my requirements.
The Search Mouse SNP between strains tool will return any SNPs that are different between strain BALB/c and strains 129 or C57BL. It does not work for your query where SNPs have to be common between strains129 and C57BL and different from BALB/c.
The way to get around this problem is to perform two searches:
First, perform a search using the Search Mouse SNP between strains tool, where you ask for those SNPs that are different between reference strain BALB/c and strains 129/Sv, 129X1/SVJ, 129X1/SV, C57BL/6, C57BL/6J, and Mus musculus C57BL/6J. Then perform a second search using the Search Mouse SNP between strains tool, where you ask for those SNPs that are found in common between reference strain 129/Sv and strains C57BL/6, C57BL/6J, and Mus musculus C57BL/6J.
Save the results from each search file in the brief format, and then filter for the SNPs (rs#) that are in both files.
- Searching for SNPs between Mouse Strains - SNP FAQ ArchiveSearching for SNPs between Mouse Strains - SNP FAQ Archive
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