How do you check if they have a start or a stop codon? When I obtain the protein sequences of the ORFs, using gffread, I see they don't start with the amino acid methionine and don't have a "dot" on the end of the sequence, which represents the stop codon on the gffread fasta output. I am sure they don't have a start and/or stop codon, I visualized them using the software Artemis.
And are you taking into account if the coordinates are 0-based or 1-based? It's 1-based.
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How do you check if they have a start or a stop codon? When I obtain the protein sequences of the ORFs, using gffread, I see they don't start with the amino acid methionine and don't have a "dot" on the end of the sequence, which represents the stop codon on the gffread fasta output. I am sure they don't have a start and/or stop codon, I visualized them using the software Artemis.
And are you taking into account if the coordinates are 0-based or 1-based? It's 1-based.
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