text: user16218: Can prokka be used to annotate a set of protein sequences (so bulk protein annotation), or does it require an entire genome for the annotation?
  I've been looking through the documentation but haven't found a clear answer to this. I tested it, and the annotation of my protein sequences worked, but I wanted to check if the program expected a genome and that I can trust the output.
  Thanks!
  
  user252: Prokka doesn't need whole genomes, I've definitely used it for smaller contigs before so I think you're fine!
  
original_text: 16218: <p>Can prokka be used to annotate a set of protein sequences (so bulk protein annotation), or does it require an entire genome for the annotation?</p>
  <p>I've been looking through the documentation but haven't found a clear answer to this. I tested it, and the annotation of my protein sequences worked, but I wanted to check if the program expected a genome and that I can trust the output.</p>
  <p>Thanks!</p>
   252: <p>Prokka doesn't need whole genomes, I've definitely used it for smaller contigs before so I think you're fine!</p>
  