text: user1684: I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1).
  I ran those sequences on Prokka and RAST Seed server at the same time. I can see that only a few (may be around 1%) of the genes were annotated. Most of them were predicted as hypothetical protein. And the results were comparable between Prokka and RAST.
  I would assume that these tools look for similar sequences in NCBI and find the best-match protein. But looks like that is not the case.
  I am looking for prediction tool(s) that will:
  
  find a well annotated swinepox virus genome in Genbank to predict most of the proteins.
  improve on the prediction of Prokka and Rast to assign functions to otherwise hypothetical protein
  
  Would prediction tools such as Genemark or other genome annotation tools be beneficial.
  Alternatively have I misunderstood the concept of annotation?
  Assistance would be very welcome.
  I have attached the image for comparison. Left one the Swinepox genome in .gb format and right one is the same genome annotated with Prokka.
  
  
  user581: Both of the annotation tools you used are designed for prokaryotic genome annotation. I would not expect them to work very well for viruses. 
  
  user1684: I was able to get good annotation using prokka by using following commands in prokka.
  prokka --proteins reference.gb --outdir annotation  --prefix myprotein contigs.fa
  
  All the reading frames were annotated. Actually the ones that are hypothetical in reference genomes are also annotated. 
  
  user2580: If you are looking for another tool, you could try eggnog mapper: it is an annotation tool based on orthology assignments. The EggNOG database happens to have a section for viral Orthologous Groups so you might obtain better results with it.
  Note that emapper annotates coding sequences, not whole genomes. You need an extra step to predict CDS, for instance using Prodigal.
  Basic usage with the optimized database for viral models:
  prodigal -i my.genome.fna -o my.genes -a my.proteins.faa
  
  then
  python emapper.py -i my.proteins.faa --output polb_viruses  -d viruses
  
  
original_text: 1684: <p>I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank <em>(NCBI Reference Sequence: NC_003389.1)</em>.</p>
  <p>I ran those sequences on Prokka and RAST Seed server at the same time. I can see that only a few (may be around 1%) of the genes were annotated. Most of them were predicted as hypothetical protein. And the results were comparable between Prokka and RAST.</p>
  <p>I would assume that these tools look for similar sequences in NCBI and find the best-match protein. But looks like that is not the case.</p>
  <p>I am looking for prediction tool(s) that will:</p>
  <ul>
  <li>find a well annotated swinepox virus genome in Genbank to predict most of the proteins.</li>
  <li>improve on the prediction of Prokka and Rast to assign functions to otherwise <strong>hypothetical protein</strong></li>
  </ul>
  <p>Would prediction tools such as Genemark or other genome annotation tools be beneficial.</p>
  <p>Alternatively have I misunderstood the concept of annotation?</p>
  <p>Assistance would be very welcome.</p>
  <p><em>I have attached the image for comparison. Left one the Swinepox genome in .gb format and right one is the same genome annotated with Prokka.</em></p>
  <p><a href="https://i.stack.imgur.com/eefc1.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/eefc1.png" alt="Image : sorry for the low quality screenshot" /></a></p>
   581: <p>Both of the annotation tools you used are designed for prokaryotic genome annotation. I would not expect them to work very well for viruses. </p>
   1684: <p>I was able to get good annotation using prokka by using following commands in prokka.</p>
  
  <pre><code>prokka --proteins reference.gb --outdir annotation  --prefix myprotein contigs.fa
  </code></pre>
  
  <p>All the reading frames were annotated. Actually the ones that are hypothetical in reference genomes are also annotated. </p>
   2580: <p>If you are looking for another tool, you could try <a href="https://github.com/jhcepas/eggnog-mapper" rel="nofollow noreferrer">eggnog mapper</a>: it is an annotation tool based on orthology assignments. The EggNOG database happens to have a section for <a href="http://eggnogdb.embl.de/#/app/viruses" rel="nofollow noreferrer">viral Orthologous Groups</a> so you might obtain better results with it.</p>
  
  <p>Note that emapper annotates coding sequences, not whole genomes. You need an extra step to predict CDS, for instance using <a href="https://github.com/hyattpd/Prodigal" rel="nofollow noreferrer">Prodigal</a>.</p>
  
  <p>Basic usage with the optimized database for viral models:</p>
  
  <pre><code>prodigal -i my.genome.fna -o my.genes -a my.proteins.faa
  </code></pre>
  
  <p>then</p>
  
  <pre><code>python emapper.py -i my.proteins.faa --output polb_viruses  -d viruses
  </code></pre>
  