Retrieve DNA/amino acid sequences from HUMAnN output

Microbial community profiling HUMAnN
1

Hi.

I performed HUMAnN analysis and I found some interesting enzymes. Now I want to get the specific DNA/amino acid sequences for these enzymes which my sample has. Is it possible with the outputs HUMAnN generates? I’m not sure if temp file custom_chocophlan_database.ffn is the file I’m looking for, because it does not include all UniRef IDs present at genefamilies file.

Thanks in advance.

2

Anyone know hot to get these DNA/amino acid sequences of the enzymes?

3

Sorry for the slow reply. If the mappings are to a UniRef assigned to a species, e.g. UniRef_ABC|Species_XYZ, then you ought to find the corresponding sequence in the custom database file you cited. If the UniRef is assigned to unclassified, e.g. UniRef_ABC|unclassified, then the mapping was done at the protein level to the UniRef database itself. In that case you can look up the individual protein sequence by searching for “ABC” on the UniProt website (“ABC” is a SwissProt identifer in this analogy).

4

Thanks for your detailed explanation!