I am a wet-lab biologist with limited knowledge about scripting and programming. Now I am preparing a flat file for functional annotation of a draft fungal genome that I have deposited earlier at EMBL. I tried both gff3toembl and emblmygff3, but it seems they both do not like a draft genome. Do you know any scripts that work well with a draft genome with ca. 1000 contigs?
I am also thinking to deposit protein sequences instead of nucleotide sequence, but I am not sure if possible. Has anyone tried with protein sequences before?
All comments and suggestions are greatly appreciated!