In various projects concerning prokaryotic organisms – such as pathogen detection or surveying environmental samples – researchers commonly obtain 16S ribosomal RNA (16S rRNA) sequences. Searching BLAST® databases with newly-obtained 16S rRNA sequences will aid you in identifying and verifying organisms in your sample.

Generally, we recommend that you first search the 16S ribosomal RNA sequences database (Bacteria and Archaea). This is a small database (see the current number of records in the Nucleotide database) that contains only curated 16S rRNA sequences from the NCBI Reference Sequence (RefSeq) Targeted Loci project. In the curation process NCBI staff assure that the collection contains good quality sequences from type materials and that bacteria/archaea names are current. 
To search the database, follow these steps:

• On the BLAST home page select the Nucleotide BLAST suite.
• Select 16S ribosomal RNA sequences database (Bacteria and Archaea) from the Database pull-down menu located in the Choose Search Set section of the blastn page.
• Use the Enter Query Sequences box to enter one or multiple sequences in the FASTA format.
• Click the BLAST button to run the search without adjusting any Algorithm parameters.

If you want to expand your search to include non-curated 16S rRNA sequences, set the Database selection in the above steps to Nucleotide collection (nr/nt). Additionally, set the Organism filtering for Bacteria or Archaea or any other taxonomic group as you want.