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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?

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  • $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    Commented Mar 28, 2018 at 20:24
  • $\begingroup$ Yes, the position in the protein and the sequence are extracted from the PDB file. What do you suggest? $\endgroup$
    – Adrian Smith
    Commented Mar 29, 2018 at 9:36
  • $\begingroup$ 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. $\endgroup$
    – Devon Ryan
    Commented Mar 29, 2018 at 9:55

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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.

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