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Question: amino acid alteration position for SNPs using biomart
1
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Hi,

Is there a way by which I can get the location of amino acids alteration for some snps

     library(biomaRt)

         ensembl<-useMart("ENSEMBL_MART_SNP")

         ensembl<-useDataset("hsapiens_snp",mart=ensembl)

        SNPs<-getBM(filters ("ensembl_gene"),attributes=c("refsnp_id","ensembl_peptide_allele","ensembl_peptide_allele"),values=("ENSG00000197506"),mart=ensembl)

    head(SNPs)

rs45525131                    R/Q
rs45529242                       
rs45560337                    D/H

Is there a way by which I can get the location of this amino acids in the protein sequence of relevant gene?

Thanks

ADD COMMENTlink 20 months ago tarek.mohamed • 250 • updated 20 months ago Benn 6.9k
2
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You can add "translation_start" to your attributes.

Your code is not completely reproducible, so I changed a little bit.

ensembl<-useMart("ENSEMBL_MART_SNP")

ensembl<-useDataset("hsapiens_snp",mart=ensembl)

SNPs<-getBM(filters="ensembl_gene",attributes=c("refsnp_id","ensembl_peptide_allele","translation_start","consequence_type_tv"),values=("ENSG00000197506"),mart=ensembl)

head(subset(SNPs, consequence_type_tv=="missense_variant"))
     refsnp_id ensembl_peptide_allele translation_start consequence_type_tv
205 rs10868138                    Y/C               113    missense_variant
255 rs11140503                    P/Q               221    missense_variant
348 rs11568388                    G/R               367    missense_variant
359 rs11568398                    R/H               585    missense_variant
362 rs11568401                    R/K                 4    missense_variant
365 rs11568403                    S/T                 5    missense_variant
ADD COMMENTlink 20 months ago Benn 6.9k
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Thanks for the reply ! It was really helpful

ADD REPLYlink 20 months ago
tarek.mohamed
• 250

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