Include nucleotide substitution for point mutations

[flashton2003]

Hello,

For organisms that have point mutation detection supported, amr-finder-plus reports the amino acid change (e.g. S83F for QRDR mutations for Salmonella).

Would it be possible to also report the nucleotide change as well?

Thanks,

Phil

[vbrover]

We get point mutations from literature, and usually amino acid point mutations are not duplicated as nucleotide point mutations.
We cannot transform amino acid point mutations into nucleotide point mutations because of codon synonymity.
Besides that, biologically, these mutations work at protein level, not at nucleotide level.

[evolarjun]

I think Phil is referring to the AMRFinderPlus output identifying and outputting the nucleotide mutation when AMRFinderPlus is run on a query sequence with an amino-acid mutation.

If that is the case, it is possible to add such a feature to AMRFinderPlus, though a little bit difficult because we'd have to go back to the nucleotide from the protein sequence using the alignment and the coordinates indicated in the GFF, cut out the two codons and report any differences. Such a thing wouldn't, of course, be possible from protein-only queries.

An alternative in the meantime would require some post-processing (basically the same as we'd build into AMRFinderPlus), but you could use the --nucleotide_output option to get the DNA sequence for all of the AMRFinderPlus hits and subseq the FASTA entry to get the specific nucleotide point mutations you're after.

@flashton2003 am I interpreting your query correctly?

[flashton2003]

Hi both,

Sorry for the slow reply.

@evolarjun - yes, you're interpreting correctly. Great news about the --nucleotide_output option, I can definitely get the information I want from that.

Might be a nice feature to have anyway, but certainly not vital considering that it's quite straightforward for a bioinformatician to extract the info from --nucleotide_output.

Thanks for your quick responses.