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MIrROR User's Guide

Users can search for 16S-23S rRNA operon information by the genome in two ways on the ‘MIrROR’ page.


① Users can enter the accession number or taxonomic name of the genome in the search field. Enter the desired genome information and click the ‘magnifying glass’ button. When entering the accession number, remove the version information and prefix (ex. ‘000009345’ instead of ‘GCA_000009345.1’). Taxonomic name is searched based on both NCBI and GTDB taxonomy information.

② If you are unsure of the spelling of a particular taxon, please use ‘Browse Taxonomy’. Taxonomic name is assigned based on GTDB taxonomy. If the higher taxonomic level is specified, only the corresponding lower level can be searched. If you want to reset, click the ‘Reset’ button.


③ (①>’magnifying glass’ button, ②>’Search’ button)
The information of the genome is summarized in pie charts.
  • Assembly Level: Assembly level based on NCBI genome assembly.
  • Primer binding site: Variation of the identified primer binding site (Primer binding sites are presented in pairs. 16S-27F: 5’-AGRGTTYGATYHTGGCTCAG-3’ and 23S-2241R: 5’-ACCRCCCCAGTHRAACT-3’).
  • Taxonomy: Taxonomic name based on GTDB.



④ 16S-23S rRNA operon information for each genome are listed in a table
  • Accession: NCBI genome accession number.
  • Assembly level: NCBI genome assembly level.
  • Operon copy number: Information on the operon copy number in the genome. Please see the summary on the ‘MIrROR’ page for more details.
  • Length: Size of 16S-23S rRNA operon sequence.
  • Primer binding site: Sequence of primer binding site.
  • NCBI taxonomy: Taxonomic name based on NCBI taxonomy.
  • GTDB taxonomy: Taxonomic name based on GTDB taxonomy. You can check the release information on the ‘Download’ page.

⑤ Users can download information about searched records.
  • CSV: Download the ④ table in csv format.
  • FASTA: Download the 16S-23S rRNA operon sequence of the searched genome.
  • Search: Users can search within results.



⑥ (④>accession number)
Users can see more information about each genome in a new window. NCBI genome assembly site is accessed through ‘NCBI link’. If you want to check each 16S-23S rRNA operon sequence information, click the ‘+’ button in the space.

1. What is MIrROR?

MIrROR is a platform built to enable metagenomics analysis using 16S-23S rRNA operon sequences. MIrROR provides a manually curated database for bacterial 16S-23S rRNA operon sequence and analysis tool that profiles bacterial communities based on mapping strategy. It also provides taxonomic profiling results for the 16S-23S rRNA operon study on NCBI BioProject.

2. I performed PCR amplification with another primer. Can I use MIrROR?

MIrROR was built primarily for metataxonomics and collected sequences based on 27F/2241R, which is most commonly used in 16S-23S rRNA operon analysis. If you use PCR primer that targets the interior region of PCR products from 27F/2241R, you can use MIrROR database without any problems. However, if the reverse primer is located further to the right than 2241R primer, only information except for the region added to the right can be analyzed using MIrROR. If a new PCR primer is introduced and used frequently, it will be reflected in the MIRROR database release update.

3. Why is there no information on Helicobacter pylori’s 16S-23S rRNA operon?

Recent studies have shown that there are species whose operon system is broken by the separation of the 16S rRNA gene and the 23S rRNA gene. This includes Helicobacter, Buchnera, Borrelia, Rickettsia, Thermus, Wolbachia, etc. (See here for more details on unlinked rRNA genes.)

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