MIDORI2 GB265 / Metazoan mitochondrial 15 genes
MiFish_DB v50 by T. Sado · Source and citation (PMiFish3.0)
PR2 v5.1.1 (BLAST only): SSU rRNA, mainly eukaryotic 18S; also includes bacterial, archaeal and organellar sequences.
Example: 10 quality-filtered V4 forward reads (300–301 bp) from Wu et al. (2024), SRR27126345. These are environmental sample reads, not denoised ASVs or ten distinct species. FASTA · Provenance
PR2 labels such as sp. or _X do not identify named species. Database changes replace the example only if the input is unedited.
Please cite Guillou et al. (2013) · Source · License (PR2 repository)
Search results
Download CSVAbout the result columns
Japanese names are provided using Sname_Jname.txt from PMiFish3.0.
BLAST:
The 1st, 2nd, and 3rd hits follow the BLAST output order. Each hit includes the scientific name, Japanese common name, percent identity, and Query_coverage. Num_blastHits is the number of hits read (up to 5). Queries with no hits show 0 hits and empty result fields.
For compatibility with existing CSV files, Query_coverage means 100 minus the gap percentage, rather than coverage of the full query sequence. For MIDORI, MiFish and PR2 hits with multiple alignments, values from the last alignment are used. The added rbcL, ITS and SILVA searches use the best alignment per reference hit. Labels such as uncultured bacterium or environmental sample names are not species-level identifications.
BAYES (restricted access):
Bayes uses mothur 1.48.6: Wang method, k-mer size 8, bootstrap cutoff 80, 100 iterations, and seed 19760620. Genus and species bootstrap values indicate classification support, not BLAST identity. Unclassified labels mean the cutoff was not met. The combined 15-gene reference is used for this comparison; classifications should be evaluated for your target gene.
Bayes result files and logs are saved in a separate work folder for each run. Save your CSV: work folders may be removed after 3 days.