Functional Gene Analysis with a Protein Database in Qiime2

User Support
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Hello guys,

I got stuck in a dead-end path. I need your guidance.

I have been analyzing a functional gene for a couple of months. The result was unacceptable with the database extracted from NCBI because there were too low defined taxa. Today, I blasted the rep-seq with BLASTx. The result made my day. Now, I need to switch to protein analysis instead of DNA-based analysis, and also I need to know how can I work with protein sequences by QIIME2. I believe that no one has started such a thing with Qiime2. Anyway, It needs a protein database instead of DNA one. And I have only DNA sequences and OTUs table in available, generated with DADA2.

My questions:
Can I analyze a functional gene in QIIME2 with a protein database?
Can I extract protein database with the Rescript plugin in Qiime2?
And eventually if I start my analysis based on a protein database, how can I deal with the feature-table and ref-seq obtained DADA2, which they are constructed based on DNA sequences?

Please share your valuable suggestion with me.

Thank you very much.

Qiimer

2

Hi @TurboQiimer ,
QIIME 2 does not yet have a blastx method. We only recently added support for protein types, but there is not yet any functionality to do anything meaningful. This will change sometime in the future (you can search the forum archive for some relevant discussions of future plans) but right now it is not possible.

No and no. These are both planned for the future (possibly later this year) but not yet. You can check the release notes on this forum to keep track of when relevant functionality is added to QIIME 2. For RESCRIPt functionality, keep an eye on the release notes on the github page.

For now you will need to do these analyses (e.g., blastx) outside of QIIME 2.

Good luck!

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