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
Try this:

Download the [bacterial SSU][1] model from RFAM: https://rfam.org/family/RF00177#tabview=tab9
Then use the .cm file with the tool cmsearch of the [Infernal suite][2] to locate the SSU in the genome, extract the genome sequence at the 
best scoring coordinates and submit to NCBI Blast or blast against SILVA. You can repeat that with the LSU as well if you like. If you want to blast the rest of the genome to gain further confidence, then you can use the taxon obtained by SSU search to restrict the blast taxon range and thereby speed up the blast search.
 
Hope this works out for you.

  [1]: https://rfam.org/family/RF00177
  [2]: http://eddylab.org/infernal/