Downloading 16s rRNA sequence for all bacterial species

Question

[asharuthra]

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

[cpad0112]

ftp://ftp.ncbi.nih.gov/blast/db/

[lars.snipen]

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...

Answer 1

[Mensur Dlakic]

• https://www.arb-silva.de/
• https://ftp.arb-silva.de/current/Exports/

[5heikki]

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

Answer 2

[Congmin Xu]

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