Hello everyone,
I'm trying annotate a genome using the annotations available from Genbank. I've downloaded the genbank file and gotten bowtie2 working, with indices for my genome of interest. However, I'm not sure where to go from here. I've tried aligning them as if the annotation were a genome but that doesn't work since the annotations are not FASTA/Q file files. Alternatively I could try this in R, but again, I have no idea where I'd even begin.
I'm not really looking for any specific code to type in, more just what tool I should use to do this annotation, and I can probably figure it out from there. Any help would be greatly appreciated, thank you!
What does that mean? You are trying to annotate your own genome using annotations from GenBank for a similar genome?
Yes, this is what I'm trying to do. I'll edit my question to make that more clear.
Got it. Change the title while you are doing the edit accordingly.
Take a look at RATT.
Prokaryote or eukaryote genome?
Viral! It's Epstein-Barr Virus
So your sequence should be very similar (as long as correctly sequenced/assembled) to the one in GenBank. Align the entire genome (no need for bowtie2) using mauve.
Oh this is a great tool with clear instructions, and it even has a GUI. Thanks so much, I think this is going to help a lot.
Are you specifically bothered about carrying over an exact annotation from a specific genome? A de novo annotation will pick up most if not all of the existing annotations features if they are the closest ones anyway, so you don't need to fiddle with this necessarily