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This tool will query taxonomy reference databases for Fungi and Animals

ITS sequences for Fungi will be queried against the UNITE Species Hypothesis General FASTA release (a reference database for DNA barcoding of Fungi)

COI sequences for Animals will be queried against a 99% clustered version of the International Barcode of Life project (iBOL) public data (COI-5P sequences)

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

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References

UNITE Community (2019): UNITE general FASTA release for Fungi 2. Version 18.11.2018. UNITE Community.
The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). Occurrence dataset accessed via GBIF.org on 2019-09-26.
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).
Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D. (1990). Basic local alignment search tool. Journal of Molecular Biology. 215 (3): 403–410.
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;

Your data have been matched against a blast database of the UNITE Species Hypothesis General FASTA release. 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 International Barcode of Life project (iBOL) 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.

Match types

{{ 'BLAST_EXACT_MATCH' | prettifyEnum }} identity >= 98.5% and queryCoverage >= 80%. This is within the threshold of the OTU.
{{ 'BLAST_AMBIGUOUS_MATCH' | prettifyEnum }} {{'identity >= 98.5% and queryCoverage >= 80%, but there is at least one more match with similar identity'}}
{{ 'BLAST_CLOSE_MATCH' | prettifyEnum }} {{'identity < 98.5% 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.
{{ '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)
{{ species.sequence }}

Exclude unmatched

generate CSV
Blasting sequences - hang on 


                        

                            
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