Currently I'm working on a plant genome annotation work. For my plant, I don't have any RNA sequences or ESTs. Also very little ESTs and RNA sequence data from closely related species. Is it okay to use both closely related and somewhat distantly related species EST data and RNA seq data for gene prediction?
If not, is there any options I can follow instead of above method?
(I'm planning to use proteins sequences as well along with ESTs and RNA seqs).
Yes it will do. However, it would be more accurate if you manage a way to annotate based on protein sequences. For this you have to perform gene prediction first followed by annotation of the CDS/transcripts.
@ Kangkon Saikia Thanks so much for your answer. Yes, I'm using protein sequences as well. It will be really helpful if you can explain this part in your answer a bit more. "For this you have to perform gene prediction first followed by annotation of the CDS/transcripts."
Thanks again!
- Badges
- Science method