problem with stopcodons in-frame encoding selenocysteine

[MiSchwabe]

Hi,

I have a problem to extract the proper faa sequences if selenocysteine (U) is encoded by TGA/TAG in the CDS.
Bakta was used for the annotation and my colleague only saved the GFF3, GBK and genome file. So I used gffread (-y) to get the protein sequnces.
This resulted in a "." in the middle of mutliple preotein sequences. Is there any option to prevent this?

Best,
Michael