Download as .csv

cancel

This tool will query a blast database of the UNITE Species Hypothesis General FASTA release (a reference database for DNA barcoding of Fungi). All returned matches will then be matched against the GBIF backbone taxonomy by their identifier (e.g. SH191277.07FU). These OTU identifiers can be used for publishing sequence based data to GBIF. When the matching is complete, the result can be downloaded as a csv with identifiers included.

Only ITS sequences are currently supported.

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

{{'nameParser.dropHere' | translate}}

Cannot read file

{{ vm.error }}

References

UNITE Community (2017): UNITE general FASTA release. Version 01.12.2017. UNITE Community.
Kõljalg, U. et.al. (2013). Towards a unified paradigm for sequence‐based identification of fungi. Molecular Ecology. 22 (21): 5271-5277.
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 Species Hypothesis General FASTA release. All returned matches have then been matched against the GBIF backbone taxonomy by their identifier (e.g. SH191277.07FU). These OTU identifiers can be used for publishing sequence based data to GBIF. The result can be downloaded as a csv with identifiers included.

Sequences were assumed to be in the ITS region.

Match types

{{ 'BLAST_EXACT_MATCH' | prettifyEnum }} identity >= 98.5%. This is within the threshold of the OTU.
{{ 'BLAST_AMBIGUOUS_MATCH' | prettifyEnum }} {{'identity >= 98.5%, but there is at least one more match with similar identity'}}
{{ 'BLAST_CLOSE_MATCH' | prettifyEnum }} {{'identity < 98.5% but > 90%. It is something close to the OTU, maybe the same Genus.'}}
{{ 'BLAST_WEAK_MATCH' | prettifyEnum }} {{'there is a match, but with identity < 90%. 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.matchType | prettifyEnum }} {{species.scientificName}} (not in GBIF taxonomy) {{ species.sequence }}

Exclude unmatched

generate CSV
Blasting sequences - hang on 


                        

                            
Alternatives: