does Silva 138 99% OTUs full-length sequences pre-trained classifier work with 18s sequences?

[SoilRotifer (Mike Robeson)]

Hi @sabitondo,

@sabitondo

does the Silva 138 99% OTUs full-length sequences pre-trained classifier work with 18s sequences?

Yes the SILVa SSU database contains both the 16S and 18S rRNA gene sequences.

@sabitondo

I was able to click on each feature and blast it, and I got 100% identity matches that made sense. What gives?

What was the orientation of the query sequence in the BLAST results? I ask because, the your query sequences must be in the same orientation as classify-sklearn for it to work. If not, you'll likely observe that the returned taxonomy assignments are either spurious or unclassified. One good test would be to use classify-consensus-vsearch, which orientation of your query sequences won't matter. However, orientation will be an issue when trying to construct a phylogeny.

Also, you can try your hand at curating the SILVA database for your own needs via the RESCRIPt plugin, as outlined here, to make sure the curation approach outlined there did not unduly remove any important reference sequences.