Click on a polygon to display the list of corresponding species
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Open a .csv file for the World maps panel to display a table with their sequences and number of mismatches on each primer
You can search species name as well as sequences on the search box, and download the full table
A high number of mismatches can lead to decrease chances of amplification
Welcome to GAPeDNA !
The app is designed to browse taxonomic coverage of online genetic database for designated metabarcoding primers, and download the sequences.
Taxa covered include freshwater and marine fish at the moment.
Here is how the data is generated:
Important: Sequences in online databases must have the primer sequences, otherwise they will fail to be in-silico PCR amplified.
This might lead to under-estimated taxonomic coverage if many sequences are present but lack primers. Sequences are amplified if primer sequences have up to 3 mismatches maximum, for each primer.
Contributions to GAPeDNA:
We can expand the taxonomic breath covered by GAPeDNA with your help.
If you have spatialized checklists and/or a list of metabarcoding primer pairs for additional taxonomic groups freely available, please contact me, I can update the app and include it.
E-mail: virginie[.]marques[at]cefe.cnrs.fr
Checklist source data:
- Marine fish:
The marine fish foodweb is globally connected- Freshwater fish:
A global database on freshwater fish species occurrence in drainage basinsFish name were verified using the fishbase taxonomy
References
Developer and maintainer: Virginie Marques
Illustration: P. Lopez
Shiny server maintenance (CEFE): M.Q. Quidoz
GAPeDNA supports the following paper:
GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcodingSource code