Hi,

There does not seem to be a simple way to obtain the full sequence of SNP data using getSequence(). I have read similar requests here and the solution was to read 10 or 20 up/down stream BP using the filters for getBM(). However, the error messages for getSequence seem to imply that it cant be used with ENSEMBL_MART_SNP.

Basically, I want to download the full cdna associated with a gene (and SNP). I'm wondering if I should just download the sequence for the protein I'm interested in and then just modify the location affected by the SNP accordingly?

Many thanks

Ken

My apologies, what I had in mind was obtaining the full snp sequence, similar to how we obtain a proteins sequence.

mart <- useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
ENSG <- getBM(mart=mart, attributes="ensembl_gene_id", filters="hgnc_symbol", values="CTNS")

# The two lines above work ok, we setup "mart" to look at human genes and ENSG to contain the ensembl id for "CTNS" gene which is involved in the disease of interest. The line below setups "snpmart" to point to the snp database.

snpmart <- useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_SNP", dataset="hsapiens_snp")

# The line below is where I get totally lost.

seq1 = getSequence(id="CTNS",type="entrezgene",seqType="cdna", mart=snpmart)

# It maybe that you cant get cdna sequences from snp database. However, I have had a bit luck by modifying some code written by Steffen...

getBM(attributes=c("refsnp_id","snp"),filters=c("snp_filter","downstream_flank","upstream_flank"),values=list(snp[1:5,1],20,20),mart=snpmart, checkFilters=FALSE)

This allows a predefined length of cdna to be extracted around the snp. I'm not sure what  filters and attributes to use to figure out how big each snp is and thus get the entire sequence.