How to retain proteins with both start and stop codons, and remove those with internal stop codons from FASTA file ?

Question

[BioinfoBee]

Hello, Curious to know if anyone knows how to retain proteins with both stop codons and remove those with internal stop codons from FASTA file?

I noticed a number of internal stop codons in the minprot generated output file and wanted to filter them out. Kindly suggest!

Regards, B

Answer 1

[Mensur Dlakic]

You run a gene prediction program such as Prodigal and there won't be any predicted proteins with internal stop codons.

[BioinfoBee]

Thank you Mensur Dlakic but I am working with eukaryotes