Hi, I have googled a lot about this query but I could not find a suitable answer.
I downloaded some genomes from NCBI; predicted and annotated genes by prokka. But later, I found that there are few genomes that have 2-3 CDS regions of the same gene while other genomes have the same full-length gene (1245bp) with one CDS. I have aligned them by using MAUVE and figured out that these CDS are parts of one gene. (Further, I have also done blast to confirm this.)
My question is:
Sorry, I couldn't upload the MAUVE aligned figure for further clarification.
thanks
Awan
Have you checked for additional stop codons in those genes? It's not uncommon for larger CDSs to become split by mutation incorporating new stop sites.
Its not necessarily a problem, it may be a biological reality. The real question is whether those splits have rendered that protein defunct or not.
If it is an error, it might be an assembly problem, which has misincorporated an incorrect base. You could download the reads and reassemble if you want to find out, but odds are they are just real splits in real genes.
Yes, you are right there are stop codons at the end of each these newly formed CDS. But why there are newly formed stop codons? Thanks, I will definitely find out the functional ability of this protein.
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