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yphsieh / 16S-ITGDB

An integrated database for improving taxonomic classification of 16S Ribosomal RNA sequences.
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Confusing taxonomy #6

Open Setis09 opened 1 year ago

Setis09 commented 1 year ago

Hi guys! First of all thank you for doing this work. I think compiling and curating these databasets is really useful and would have been difficult. I have used this databases to do taxonomy assignation using QIIME2, it produced really nice results. But I have been trying to figure out some taxonomic classifications. The next line is a confusing classification that I can't understand:

HE584614.1.1460 bacteria;proteobacteria;gammaproteobacteria;enterobacterales;enterobacteriaceae;escherichia-shigella;streptomyces_sp.

The streptomyces taxonomy is not like that and there a few lines with classifications similar to that one. I would like to know where this IDs and classification came from?

I searched by ID in SILVA, GreenGenes and RPD. However, I didn't find this classification. I suspect it's from RPD but I don't know where to look to keep searching.

Maybe can you help me telling me where can I find this IDs?

cil6758 commented 1 year ago

Hi, Setis09: Thanks for reaching out. I searched the taxonomy you listed here and found it is in the SILVA database(version 138, 99% clustering). For some bacterial species, different databases may use different ways to express the taxonomy annotations (among RDP, SILVA, and Greengenes), but they describe the same bacterial taxonomy. Hope this helps.