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.