[maker-devel] Unknown (X) amino acids in predicted proteins

[Lior Glick]

Dear MAKER users,

After completing a MAKER run, I looked at the protein fasta files that
MAKER outputs and noticed that a small fraction of the sequences include X
characters, indicating unknown amino acids. I was wondering how such
sequences are obtained, I mean how come there are unknown amino acids in
the prediction? Is this an indication of low-quality predictions?
Is there any documentation regarding the procedure that generates the
protein sequences?

Thanks a lot,
Lior
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