could the annotated sequence as the input for gapseq about gapseq HOT 5 CLOSED

Yes, this would be great-BLASTP (or DIAMOND) would be much faster than TBLASTN based on my experience.

from gapseq.

Hi Hongzhong,

in the current Version, gapseq supports only the genome input as nucleotide fasta sequence. But I agree, a protein fasta for the annotated proteins as alternative input would be a useful extension. I will mark this as a feature request, which we will address in an upcoming version.
Until then, you could use the coding sequences of your proteins in a nucleotide fasta as gapseq input as a workaround.

Best regards,
Silvio

from gapseq.

Thanks so much! Looking forward to the new functions.

from gapseq.

Yes, we actually have plans in those directions; specifically to employ DIAMOND.
But since this is not per se an issue in the workflow, would it be okay with you to convert this conversion to the discussion forum (a new feature in github)?

from gapseq.

Definitely!

from gapseq.