Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-03-29T08:49:38.330Z
Answers.LastActivityDate: 2018-03-29T08:49:38.330Z
Answers.UserDisplayName: Emily_Ensembl
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-28T20:24:22.277Z
Comments.Text: Do you have the position in the protein from the PDB file? If so, it'd be much easier to use that then the sequence itself.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-29T09:36:43.540Z
Comments.Text: Yes, the position in the protein and the sequence are extracted from the PDB file. What do you suggest?
Comments.UserDisplayName: Adrian Smith
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-29T09:55:29.440Z
Comments.Text: Simply use the protein ID and position within the protein, as suggested by Emily_Ensembl. Blasting or blating things would be both slower and more likely to produce incorrect results.
Comments.UserDisplayName: Devon Ryan
Tags: <r><proteins><ngs><pdb><biomart>
Title: Retrieval of genomic position by using biomaRt package
ThreadText: # Retrieval of genomic position by using biomaRt package
  
  (Asked by: username_0 on 2018-03-28)
  
  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?
  
  **Tags:** r, proteins, ngs, pdb, biomart
  
  > **Comments:**
  > **username_1**: Do you have the position in the protein from the PDB file? If so, it'd be much easier to use that then the sequence itself.  
  > **username_0**: Yes, the position in the protein and the sequence are extracted from the PDB file. What do you suggest?  
  > **username_1**: Simply use the protein ID and position within the protein, as suggested by username_2. Blasting or blating things would be both slower and more likely to produce incorrect results.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-03-29. Score: 4
  
  BiomaRt cannot do that I'm afraid. There is an [Ensembl REST API endpoint](http://rest.ensembl.org/documentation/info/assembly_translation) 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](http://rest.ensembl.org/documentation/info/xref_external) 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.
  
  
  ---
  
  