Downloading 16s rRNA sequence for all bacterial species
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10 months ago
asharuthra • 0

Dear all,

I'm trying to create a custom database in Qiime 2, there i need to download the 16s rRNA sequence of all bacterial species in fasta format. can any one suggest me from where i could able to download the 16s rRNA sequence of bacteria in fasta format.

Thanks in advance

Assembly RNA-Seq 16s rRNA NGS • 1.1k views
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At this address I only found BLAST database files, no FASTA files as was asked for above. Is here a quick way of getting the FASTA file(s) behind this (from R), without running BLAST+ locally? I know I can do this manually by clicking at NCBI, but I wanted to do it directly by scripting in R...

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Silva is excellent, especially with their new license. Another good option (IMO about equal to Silva) is http://rdp.cme.msu.edu/

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10 months ago
Congmin Xu • 0

The RDP database might be another good choice (http://rdp.cme.msu.edu/misc/resources.jsp).

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