I disagree with the previous two answers. Both databases contain published sequences, and the nr database contains bacterial sequences as well. In fact, the nr/nt database contains many more bacterial 16S rRNA sequences than the 16S databse. The 16S rRNA database contains 16S sequences from named bacterial species, which are usually culturable, and well characterized. The nr/nt database, however, is much bigger, and will give you a much closer match. This is especially important if you have a sequence from an uncultivated, and yet uncharacterized bacterium. The 16S database might not give a very close match in that case. The nr/nt database is much more likely to contain very similar sequences to your unknown.

I hope this helps!

you need to search against 16s ribosomal RNA if you want bacterial homologs, if u want homologs from other sps u need to search against non redundant db i.e., nr database

Ribosomal database is the best because it has only published sequences.m

I disagree with the previous two answers. Both databases contain published sequences, and the nr database contains bacterial sequences as well. In fact, the nr/nt database contains many more bacterial 16S rRNA sequences than the 16S databse. The 16S rRNA database contains 16S sequences from named bacterial species, which are usually culturable, and well characterized. The nr/nt database, however, is much bigger, and will give you a much closer match. This is especially important if you have a sequence from an uncultivated, and yet uncharacterized bacterium. The 16S database might not give a very close match in that case. The nr/nt database is much more likely to contain very similar sequences to your unknown.

I hope this helps!

I totally agree with Elisabeth.. You should use nr database to get the best homolog of your 16S sequence.. I would add in it further. Suppose some one has deposited just genome and not 16S of any bacteria, in that case if you are searching in 16S database, you will not get a hit from that bacteria as its 16S is not there in database. But if you are searching in nr database, it will search everywhere in NCBI database and let you know the best hit from even the corner of NCBI.

But to get a specific result for ur search u need to use ribosomal why because nr database gives all the similarities n huge data

Divya, here we are not talking about being specific, here we are trying to get a best hit for our 16S rRNA. If we will use nr it will be from all the genomes available around, if we will use 16S database it will be limited and will not be the confirmed hit for our sequence.

Yeah thats right even i will agree with that

Have you tried EzBioCloud ? Somehow I found it more reliable for some sequences. I have sequences that cannot be executed well by NCBI, but could get similarity on EzBioCloud https://www.ezbiocloud.net