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This tool will query taxonomy reference databases for Fungi, Animals, Bacteria and Archaea

Files can be uploaded in CSV or FASTA format. CSVs are expected to have a columns named 'sequence', 'marker' and an 'id' or 'occurrenceId' column. It is also possible to paste sequences into the text field below (only FASTA format)

ITS COI 16S 18S 12S

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References

UNITE Community (2022):UNITE general FASTA release for eukaryotes 2. Version 2022-11-29. UNITE Community.
Nilsson, R.H. et.al. (2019). The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research. Volume 47, Issue D1, Pages D259–D264
Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. 2018. MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding. Mol Biol Evol 35:1553-1555.
Ratnasingham, S., & Hebert, P. D. N. (2013, July 8). A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. (D. Fontaneto, Ed.) PLoS ONE. Public Library of Science (PLoS).
The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). Occurrence dataset accessed via GBIF.org on 2023-03-12.
Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604.
Parks DH., Chuvochina M, Chaumeil P, Rinke C, Mussig AJ, Hugenholtz P (2020). A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology volume 38, pages 1079–1086
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P, Hugenholtz P (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology volume 36, pages 996–1004
Daniel Vaulot, Javier del Campo, Mahwash Jamy, Fabien Burki, Laure Guillou, Luciana Santoferrara, Maximilian Ganser, Andrea de Oliveira da Rocha Franco, Kenneth Mertens, Haifeng Gu, Se Hyeon Jang, Pavel Škaloud, Manon Dünn, Megan Gross, Алексей Селюк, Miguel Mendez Sandin, Sebastian Metz, Richard Dorrell, & AnnaMaria Fiore-Donno. (2023). pr2database/pr2database: PR2 version 5.0.0 (v5.0.0). Zenodo.

Your data have been matched against a blast database of the UNITE general FASTA release for eukaryotes v9.0. All returned matches have then been matched against the GBIF backbone taxonomy by their identifier (e.g. SH1571756.08FU). These OTU identifiers can be used for publishing sequence based data to GBIF. The result can be downloaded as a csv with identifiers included.

Your data have been matched against a 99% clustered version of the BOLD Public Database v2024-01-06 public data (COI-5P sequences) All returned matches have then been matched against the GBIF backbone taxonomy by their identifier (e.g. BOLD:ADJ8357). These OTU identifiers can be used for publishing sequence based data to GBIF. The result can be downloaded as a csv with identifiers included.

Your data have been matched against the Genome Taxonomy Database r214 16S rRNA gene sequences identified within the set of representative genomes

Your data have been matched against the MitoFish v3.97 database of 12S sequences

Your data have been matched against the PR2 v5.0.0 database of 18S sequences

Match types

{{ 'BLAST_EXACT_MATCH' | prettifyEnum }} identity >= 99% and queryCoverage >= 80%. This is within the threshold of the OTU.
{{ 'BLAST_AMBIGUOUS_MATCH' | prettifyEnum }} {{'identity >= 99% and queryCoverage >= 80%, but there is at least one more match with similar identity'}}
{{ 'BLAST_CLOSE_MATCH' | prettifyEnum }} {{'identity < 99% but > 90% and queryCoverage >= 80%. It is something close to the OTU, maybe the same Genus.'}}
{{ 'BLAST_WEAK_MATCH' | prettifyEnum }} {{'there is a match, but with identity < 90% or/and queryCoverage < 80%. Depending on the quality of the sequence, bit score, identity and expect value, a higher taxon could be inferred from this.'}}
{{ 'BLAST_NO_MATCH' | prettifyEnum }} No match.
{{ ( vm.matchedSequenceCount / vm.species.length) | formatAsPercentage:100 }}%
{{vm.matchedSequenceCount}} of {{vm.species.length}} sequences processed
{{ vm.species.length | localNumber }}
sequences
{{ ( vm.blastMatchCount / vm.species.length) | formatAsPercentage:100 }}%
with blast match
{{ ( vm.aboveThresholdCount / vm.species.length) | formatAsPercentage:100 }}%
with identity > {{vm.matchThreshold}}%
{{ ( vm.inBackboneCount / vm.species.length) | formatAsPercentage:100 }}%
with GBIF backbone match

{{ species }}
{{ col }} ▲ ▼
{{ species.occurrenceId }} {{ species.marker }} {{ species.identity }}% {{ species.bitScore }} {{ species.expectValue }} {{ species.queryCoverage }}% {{ species.queryLength }} {{ species.matchType | prettifyEnum }}
{{species.scientificName}} (not in GBIF taxonomy)

Exclude unmatched

generate CSV
Blasting sequences - hang on 


                        

                            
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