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Scientists developed the Reference Sequence Browser (RSB), a tool simplifying access to genetic databases for environmental DNA (eDNA) analysis. This application helps researchers efficiently find and download reference sequences for species monitoring without needing advanced computational skills.

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Area of Science:

  • Ecology
  • Bioinformatics
  • Genomics

Background:

  • Environmental DNA (eDNA) is crucial for monitoring species diversity and distribution.
  • Identifying and accessing reference sequences from multiple databases is computationally intensive.
  • Current methods require specialized bioinformatics skills, limiting accessibility for many researchers.

Purpose of the Study:

  • To develop an accessible tool for searching and retrieving reference sequences from multiple genetic databases.
  • To streamline the process of assay development for eDNA metabarcoding and quantitative PCR.
  • To facilitate the determination of reference sequence availability for target and non-target taxa.

Main Methods:

  • Iterative design of a Graphical User Interface (GUI) Shiny application named the Reference Sequence Browser (RSB).
  • Integration of data from NCBI Nucleotide, BOLD, and CALeDNA CRUX Metabarcoding Reference Databases.
  • Implementation of search filters including sequence length and country of origin.

Main Results:

  • The RSB provides efficient and intuitive access to multiple genetic databases.
  • Users can determine the number of publicly available barcode markers per organism.
  • The application allows downloading of FASTA/GenBank files and exploration of sequence availability data.

Conclusions:

  • The RSB democratizes access to essential genetic data for eDNA research.
  • It significantly reduces the time and computational expertise needed for reference sequence retrieval.
  • The tool supports more robust and efficient species monitoring and biodiversity assessment.