I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a search for “ITS2” “Panama” and “Viridiplantae” on NCBI GeneBank. For the purpose of assigning sequences of unknown plants (obtained from environmental DNA studies) based on similarity to the known sequences I want to clean up my data and present each sequence with its corresponding taxonomic ranks - Kingdom ; Phylum ; Class ; Order ; Family ; Genus; Species.
My problem is that the taxonomic information for each sequence upload in NCBI is all over the place –e.g. some sequences have additional taxonomic ranks listed in their information and there is no clear definition of what corresponds to which taxonomic rank. Since there are a few hundred species I want to refrain from filling in the information manually and I hoped to solve this problem by mining the taxonomic ranks I need from a different database according to the species or genus name in the sequence information. However, I have yet to find a dataset that is comprehensive enough to include all the plants and is simple to access. Do you have any suggestions on how to achieve my goal? Thanks.