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blast User's Guide

Users can align their query sequence or Fasta with MIrROR database using BLAST. Since the server has limited resources, it may take a long time to perform BLAST with more than 10 sequences.


① Users can perform BLAST by entering query sequences or uploading a Fasta file. Only Fasta format is supported. If you are not familiar with Fasta format, please click ‘Example sequence’. Users can name the ‘Job Title’, and BLAST is performed when click ‘Execute’ button. When a new release is released, users can select the desired release from the Dataset.



② (①>’Execute’ button)
  • Job Title: Job title.
  • RID: Request ID for retrieving results from a specific NCBI BLAST search
  • Results for: If there two or more sequences, you can select one.
  • Query Length: Size of the query sequence.
  • Program: Algorithm of BLAST search and version
  • Database count / length: Number of sequences in database and basepair.
  • Kappa / lambda / entropy: Statistical detail about the BLAST search - Kappa, lambda, and entropy values.
③ BLAST Results are shown similar to the ‘BLASTn output format 6’
  • Operon sequence: Subject sequence id.
  • Bit Score: Bit score.
  • Alignment Length: Alignment length.
  • Mismatches: Number of mismatches.
  • Query Cover: Query coverage per subject.
  • Percent Identity: Percentage of identical matches.
  • E value: Expect value.
  • GTDB Taxonomy: Taxonomic name of the subject.



④ (③>’Alignment’ tab)
Users can check the alignment between the query sequence and MIrROR database in bit score order.

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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