Nucleotide to protein and vice versa.

Question

[Bioaln]

Hello.

I've been recently dealing with a fundamental problem, related to biology - mapping from protein back to DNA. I realize this is currently not precisely possible, yet I still seem to miss some vital information regarding this subject.

If I understand correctly, for annotated exons, codon to protein mapping should be available, so mappings from genomic locations to protein sequences. Where can one find this type of information?

Thanks for any clarification.

Answer 1

[Devon Ryan]

You're misreading the uniprot page, it's trivial to go from DNA -> protein, but it's impossible to determine the DNA sequence from the protein sequence alone (you can however blast the sequence back and generally determine this...but that requires knowing the genome or transcriptome sequence). This is why one can annotate what SNPs do.

For further details, please see any basic book on genomics.

[Bioaln]

I reformulated the question, sorry for the confusion.

[Devon Ryan]

You can download everything you want from Ensembl. The gene locations are in the GTF file. The protein sequence are in "protein sequence (fasta)" files.

[Bioaln]

Aaah. I missed the fact that fasta sequences also include genome regions. This explains how to get from gene sequence to the protein sequence, yet the exact nucleotide-to-amino-acid mapping is not available if I am not mistaken? (so one-to-one mapping from nucleotide to AA)

[Devon Ryan]

There isn't always a 1:1 mapping, given overlapping transcripts, so no you won't find anywhere something like:

chromosome    position    nucleotide    amino acid
chr1          123         A             M
chr1          124         T             M
chr1          125         G             M

[Bioaln]

Thank you, this clarifies it for me.