7 months ago by
United States
Hi,
AFAIK SNP information for mouse can be found in different places via biomaRt:
1. In the snp_chromosome_strand
attribute of the mmusculus_gene_ensembl
dataset of the ENSEMBL_MART_ENSEMBL
mart:
> library(biomaRt)
> mart <- useMart(host="may2012.archive.ensembl.org",
biomart="ENSEMBL_MART_ENSEMBL",
dataset="mmusculus_gene_ensembl")
> attribs <- listAttributes(mart)
> grep("snp", attribs$name, ignore.case=TRUE, value=TRUE)
[1] "snp_chromosome_strand"
2. In the mmusculus_snp
and mmusculus_structvar
datasets of the ENSEMBL_MART_SNP
mart:
> listMarts(host="may2012.archive.ensembl.org")
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 67
2 ENSEMBL_MART_SNP Ensembl Variation 67
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 67
4 ENSEMBL_MART_VEGA Vega 47
5 REACTOME REACTOME (CSHL US)
6 pride PRIDE (EBI UK)
> snp_mart <- useMart(host="may2012.archive.ensembl.org",
biomart="ENSEMBL_MART_SNP")
> snp_datasets <- listDatasets(snp_mart)
> snp_datasets[grep("mus", snp_datasets$dataset), ]
dataset description
10 mmusculus_snp Mus musculus Variation (dbSNP128; ENSEMBL)
11 mmusculus_structvar Mus musculus Structural Variation (dbSNP128; ENSEMBL)
version
10 dbSNP128; ENSEMBL
11 dbSNP128; ENSEMBL
Hope this helps,
H.