I want to explore the antibiotic resistant genes profile in my data using the ShortBRED pipeline. The pipeline requires two input files in the first phase to make marker genes: (i) FASTA file for proteins of interest, (ii) Large reference database of protein sequences. For the first one, I am wondering how can I create or download a proteins of interest file? I want to look for all antibiotic resistant genes which may appear in my samples.

Also, I am wondering how can I create a reference database for proteins sequences (second input file) from the CARD database.