Reference Sequence Browser: An R application with a User-Friendly GUI to rapidly query sequence databases v2
Sriram Ramesh, Samuel Rapp, Jorge Tapias Gomez, Zia Truong, Dickson Chung, Benjamin Levine, Daniel Tapias-Gomez · 2024
Knowledge of which organisms have publicly available reference sequences at known DNA barcoding loci is crucial for both metabarcoding studies and the design of new primers. In a metabarcoding study, taxa of interest can not be detected if there are no labeled reference sequences to compare to. Similarly, designing species-specific primers is only possible if there are enough reference sequences for both the target taxa and their phylogenetic relatives to represent the genetic diversity across individuals. The purpose of this is to tool allow scientists to automatically gather reference sequences from NCBI, BOLD and CRUX. It is important to note that this is just a in-depth guide on how to use the tool, for more details on the features and their importance please refer to our paper in: https://doi.org/10.1371/journal.pone.0309707