We have a curated set of ribosomal RNA (rRNA) reference sequences (Targeted Loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples (Table 1). To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms (Figure 1)
|16S ribosomal RNA (Bacteria and Archaea)||PRJNA33317 , PRJNA33175
|18S ribosomal RNA sequences (SSU) from Fungi type and reference material||PRJNA39195||2,337|
|28S ribosomal RNA sequences (LSU) from Fungi type and reference material||PRJNA51803||5,185|
|Internal transcribed spacer region (ITS) from Fungi and Oomycete type and reference material||PRJNA177353, PRJNA362621
Table 1. NCBI curated targeted rRNA sequences now available as BLAST databases.
Figure 1. The database selection menu on the nucleotide-nucleotide BLAST page with the rRNA/ITS database radio button selected.
Using these databases for identification will speed up your searches and provide you the most informative results. If you want to expand your search to include non-curated 16S rRNA sequences, change the to the Nucleotide collection (nr/nt) database. You may also want to set the Organism filter to your taxonomic group of interest.
You can also download these new databases from the BLAST db FTP directory for use in local BLAST searches.