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How do I use BLAST for 16S ribosomal RNA sequences to identify or verify prokaryotic organisms?

In various projects concerning prokaryotic organisms, such as pathogen detection or environmental sample survey, 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 present in your sample.

We recommend that you search 16S ribosomal RNA sequences database (Bacteria and Archaea). This is a small database containing only NCBI-curated 16S rRNA sequences. This collection contains good quality sequences from type materials. NCBI also ensures that bacteria/archaea names in the database are current.
 

To search the database, follow these steps:

  • On the BLAST home page select the Nucleotide BLAST suite.
  • Use the Enter Query Sequences box to enter one or more sequences in the FASTA format.
  • In the Choose Search Set section, switch the radio button selection from the default Standard databases (nr etc.) to rRNA/ITS databases. (The pull-down menu below the selection will refresh in the subsets of rRNA/ITS databases.)
  • Select the 16S ribosomal RNA sequences (Bacteria and Archaea) database.
  • Click the BLAST button to run the search without further adjustment.

 

Can you expand your search to non-curated 16S rRNA sequences?


Yes. You can switch back to the Standard databases (nr etc.) radio button which will adjust the menu of available databases. Use Core nucleotide database (core_nt). Given the large number of 16S rRNA sequences in these databases, we recommend that you narrow your search by organisms (taxonomic groups). For that, use the Organism field below the database menu.

 

Where can you learn more?
 

BLAST documentation:


RefSeq documentation:
Knowledge articles: