Can Qiime assign taxonomy to proteins?

[iquasere (João Sequeira)]

I am trying to run Qiime2 to taxonomically annotate proteins. So far, I have run this command to import a FASTA as a Qiime object:

qiime tools import --type "FeatureData[ProteinSequence]" --input-path protein_fasta_qiime2_test/non_chimeric_prot_corr_q2_import_test.fasta --output-path sequences.qza

and have tried running this command to classify the sequences

qiime feature-classifier classify-hybrid-vsearch-sklearn

but it doesn't accept "FeatureData[ProteinSequence]" as a valid input format. How can I classify protein sequences taxonomically with Qiime2? Also, would it be preferable (faster or more accurate) to common methods with BLAST or DIAMOND?

[Nicholas_Bokulich]

Welcome @iquasere !

QIIME 2 cannot currently assign taxonomy to proteins. It is a work in progress to add this functionality (contributions are very welcome! ), see here for more details and relevant discussion:

Importing protein sequences into version 2021.2

Hi q2-team! I was excited to see the 2021.2 version including q2-types that can read proteins/amino acid sequences. But I am getting errors importing an unaligned .fasta file, which contains typical fasta headers and amino acid sequence lines. I reference this announcement about protein types (QIIME 2 2021.2 is now available). Can I confirm the formats/q2-types listed in the announcement are immediately available? For instance, when running a qiime tools import command, it yields an error: No …