Import amino acid sequences in QIIME2

Hi everyone,

I am working on homologous amino acid sequences of a functional protein. It makes more sense to analyze the data in the amino acid level rather than nucleotide level because the nucleotide sequences of the product are highly diverse while the amino acid sequences are relatively more conservative and only have diversity in certain regions. I’d like to analyze my amino acid sequences using the features (OTUs, a sequence and a variant and etc) analysis method of QIIME2. However, it seems that I can only either analyze the data in nucleotide level with the features or analyze the data in amino acid sequence level by importing OTUs. In this case, I will have to miss the other features of my data. Some people had similar questions in the beginning of 2018: Import amino acid sequences?. I wonder if there is any progress about importing amino acid sequences in QIIME2 right now.
Thank you.


Hello Karren,

I’m glad you found that thread, as the status of protein analysis in qiime is the same; we don’t fully support it yet.

Keep in mind that the upstream processing steps like denoising and clustering and chimera checking will be totally different for proteins and DNA. (I can’t imagination a reason to ever use chimera checking on a peptide). However, the downstream analysis once you have the feature-abundance table will be exactly the same; you can compare the alpha diversity of microbes and peptides in exactly the same way.

So while Qiime just doesn’t work with proteins in the initial processing steps, it should work great if you simply import your ‘OTU table’ that’s full of peptide abundances and use Qiime 2 for all the statistical analysis.



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