Will qiime2 support functional gene analysis in the future?

[colinbrislawn (Colin J Brislawn)]

Right now, Qiime only supports DNA/RNA and not Amino Acid data. Mark, if your database is of AA genes (and not the DNA that encodes these genes), you might have better luck outside of Qiime.

On the other hand, if you do have the DNA coding regions behind the genes, Qiime 2 would work just fine. All we would need is a good tutorial about how to use Qiime 2 with 'custom PCR primers that target custom genes.'

Given that proteomics is the future, it might be interesting to build q2-types for Amino Acids so that programs like FunGene that use AA could become Qiime2 plugins in the future. Here, the lead dev discribes why Qiime 2 is DNA only for the time being:

Import amino acid sequences?

Hi @steff1088, Good question, thanks for bringing this up. You and @colinbrislawn are correct - at the moment we don't support sequences of amino acids, but it is something that we could support. Out of curiosity, would you mind describing your use case? I'm going to assume in this message that all of your amino acid sequences are homologous with one another (i.e., they are sequences of the same protein) - if that is not the case, let me know. The reason that we currently don't allow sequences…