Taxonomy outline based on NCBI nucleotide collection (nr/nt)

Hi mothur-people,

Is there any possibility to have mothur-compatible taxonomy files of NCBI nucleotide collection (nr/nt)?
I would compare OTU consensus classification I get from using RDP and Greengenes to that using nr/nt.

I have noticed some differences between RDP and Greengenes classification especially with methanotrohic and methylotrophic bacteria and would use nr/nt as “a third opinion”. Currently I do it by megablasting the OTU repseq at NCBI:s web site. However, I would like to get the OTU consensus taxonomy also from nr/nt.

Best regards,

Dr. Antti J Rissanen
University of Jyväskylä,
The land of 187888 lakes

I’ll look into it - have you tried the updated silva taxonomy reference that we posted a few moths ago?