Question

SNPs between specific mouse strains

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9.5 years ago

Inbalor ▴ 20

Hi!

I have around 100 genes and I am really interested in knowing if these genes have SNPs described between specific mouse strains (DBA/2 and C57/BL6).

I know that you can use mouse SNP query at MGI webpage (Mouse Genome Informatics) but you can only search SNPs restricted to specific gene or by chr.

Do you know how I can search SNPs for multiple genes in different mouse strains at the same time?

Thanks a lot!

snp gene • 3.0k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Inbalor ▴ 20

Ram · Answer 1 · 2015-06-09

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9.5 years ago

Devon Ryan 104k

Personally I would just use the VCF files from the Sanger Institute. That's a nice standard format that'll make your life easier.

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Devon Ryan 104k

score 1 · Answer 2 · 2015-06-09

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9.5 years ago

joaomatos02 ▴ 10

You can try Biomart in Ensembl. I think you can compare up to 3 strains. Good luck

ADD COMMENT • link 9.5 years ago by joaomatos02 ▴ 10

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Do you have a link for this? I can't seem to find how to do it.

ADD REPLY • link 9.5 years ago by pld 5.1k

Ram · Answer 3 · 2015-06-09

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9.5 years ago

Inbalor ▴ 20

I find out that it can be used SNP/variation query at Mouse Phenome Database where you can find SNPs for 100 genes (max) at the same time.

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by Inbalor ▴ 20