GTDB is an amazing resource. I am looking at designing primers of a protein coding gene to look at strain -level diversity of a clade and thought I could use GTDB to check across >100 marker genes for good candidates for primer design.
From what I can work out from the current download page
bac120_msa_marker_genes_reps is the trimmed and aligned marker gene for the GTDB representatives. From the method outlined,
hmmer uses amino acid sequences instead of nuclotides, so I was wondering if I could reverse translate these back into their nucleotide sequences?
Has anyone tried this before? Could this be done by feeding
bac120_msa_marker_genes_reps and the nucleotide version of
bac120_marker_genes_reps into a tool such as pal2nal?
Any tips appreciated.