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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

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Cannot read file

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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
Kõljalg, U. et.al. (2013). Towards a unified paradigm for sequence‐based identification of fungi. Molecular Ecology. 22 (21): 5271-5277.
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.
Palmer JM, Jusino MA, Banik MT, Lindner DL. 2018. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925;
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
Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D. (1990). Basic local alignment search tool. Journal of Molecular Biology. 215 (3): 403–410.

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 v2023-03-12 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 r207 16S rRNA gene sequences identified within the set of representative genomes

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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