text: user1847: I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files).
  I'm looking for the genomic position (triad of translated nucleotides) of a specific amino acid in the sequence (i.e. residue number 64 in a protein sequence of 344 amino acids).
  Is it possible to BLAT an amino acid sequence by using biomaRt in R? 
  Do you suggest other methods to achieve this task?
  
  user1332: BiomaRt cannot do that I'm afraid. There is an Ensembl REST API endpoint that will get you the genomic location of protein coordinates. It needs an Ensembl peptide ID an input though, so you could use the xref endpoint first to get that. There's a bit of sample code in R on those pages, you could use that to script together if you've got a list of these.
  
original_text: 1847: <p>I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files).</p>
  
  <p>I'm looking for the genomic position (triad of translated nucleotides) of a specific amino acid in the sequence (i.e. residue number 64 in a protein sequence of 344 amino acids).</p>
  
  <p>Is it possible to BLAT an amino acid sequence by using biomaRt in R? 
  Do you suggest other methods to achieve this task?</p>
   1332: <p>BiomaRt cannot do that I'm afraid. There is an <a href="http://rest.ensembl.org/documentation/info/assembly_translation" rel="nofollow noreferrer">Ensembl REST API endpoint</a> that will get you the genomic location of protein coordinates. It needs an Ensembl peptide ID an input though, so you could use the <a href="http://rest.ensembl.org/documentation/info/xref_external" rel="nofollow noreferrer">xref endpoint</a> first to get that. There's a bit of sample code in R on those pages, you could use that to script together if you've got a list of these.</p>
  