How To Link Dbsnp To Its Protein Information

Question

[heath]

Hey everyone,

I see there is attributes of amino acid position in the dbSNP. Is there a way to obtain the related protein information (such as the protein fasta/gi) to the mutated position marks using biopython or entrez?

[Pierre Lindenbaum]

can you please give us a rs### as an example.

[heath]

en ....how about rsId 121434622 as an example?

Answer 1

[Pierre Lindenbaum]

use ncbi e-efetch: "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=121434622&retmode=xml"

the protein is described in the XML document:

     (...)
      <FxnSet geneId="2332" symbol="FMR1" mrnaAcc="NM_001185081" mrnaVer="1" protAcc="NP_001172010" protVer="1" fxnClass="missense" readingFrame="2" allele="A" residue="N" aaPosition="303" soTerm="non_synonymous_codon"/>
     (...)

[heath]

Thanks a lot! i will take a look of the eutils.... I thought biopython would have tools to handle dbSNP since I used biopython via entrez for the proteins information from ncbi and dbSNP is one of the nodes involved in entrez. And again from above information i can see the amino acid location, but where I get the protein information?

I mean for example it shows :aaPosition="303", but on which proteins fasta sequence?

[Pierre Lindenbaum]

you can clearly see that the ACN of the protein is NP001172010 : "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=NP001172010&rettype=fasta&retmode=txt"

[heath]

oh ..I see! Thanks a lot! figured out the eutil is a similar things to the biopython.entrez.esearch