Hi all,

I have a fasta file of an assembled genome of a bacterial strain. I would like to identify the species of this strain (or the closest one possible) using the 16s rRNA sequence. 

I tried downloading multiple 16s rRNA sequences from the NCBI database and to perform blastn analysis but I don't think I am using the most efficient method.

Do you have any recommendations on what tool to use to identify the species of a particular strain using 16s rRNA ? 

Thank you in advance for your help!

Audrey
This is a good 16S reference file:
https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_138.1_SSURef_tax_silva.fasta.gz

And the map that goes with it:
https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/taxmap_slv_ssu_ref_138.1.txt.gz

Although you may want to read the SILVA site first to determine if you want these files or perhaps e.g. a non-redundant higher quality version

https://www.arb-silva.de/

Blasting against the fasta file is fine as long as you place proper thresholds for hit reporting. Also, it will obviously be way faster if you're just blasting the 16S sequence and not the entire genome assembly (for ideas how to extract see Michael's reply)

That being said, I don't think 16S is the way to go for species identification, especially if you want strain/serotype level resolution