I have a recently developed pipeline for marker development in hand. It requires a reference protein database/fasta file, which I have. It also requires either a file containing all wikigene names/descriptions associated with this reference gene database (e.g., using Ensemble BioMart tool) or a .gtf file downloaded. In addition to the reference protein fasta file, I only have a fasta file of the nucelotide sequences, a CDS file, and a .gff3 file for the reference nucelotides but not the proteins.

How can I get a .gtf file for the proteins using the files I have available? I know of a couple ways to convert a .gff to .gtf, if needed. I just need to get the protein dataset to at least the .gff format.