Difference between downloadable and live BOLD identification databases for plant rbcL

Hi, I’m looking at plant rbcL region and am getting quite different results when using the downloadable (from BOLD) database run through Qiime2 and then using the manual BLAST on the BOLD server/website. Any ideas?

Hello David,

I’m not familiar with the BOLD database, per say. I’ll let others comment.

My guess is that Qiime is doing other quality filtering steps or using a different method for taxonomy assignment then is used on the BOLD website. In order to assess this, we could look at the steps you ran in Qiime 2 (based on the provenance in your qiime artifacts) and compare that to the data process described on the BOLD website.

If this is something you want to explore, you can post the Qiime command you can and also a link to the results from BOLD?

Using different reference databases could also change the results. I can only find old versions of the bold database but maybe you know where to download the full database you searched online.


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