Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference seque...

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Bibliographic Details
Published in:PloS one 2024-10, Vol.19 (10), p.e0309707
Main Authors: Ramesh, Sriram, Rapp, Samuel, Tapias Gomez, Jorge, Levine, Benjamin, Tapias-Gomez, Daniel, Chung, Dickson, Truong, Zia
Format: Article
Language:English
Subjects:
Analysis
Automation
Availability
Bar codes
Biological monitoring
Biology and Life Sciences
Computer and Information Sciences
Computer programming
Databases, Genetic
Databases, Nucleic Acid
Deoxyribonucleic acid
Design
DNA
DNA barcoding
DNA Barcoding, Taxonomic - methods
DNA sequencing
Ecologists
Ecology
Ecology and Environmental Sciences
Environmental DNA
Environmental science
Evaluation
Gene sequencing
Genetic aspects
Genomics
Graphical user interface
Keywords
Lab Protocol
Land management
Metadata
Methods
Nucleotide sequence
Nucleotide sequencing
Nucleotides
Organisms
People and Places
Research and Analysis Methods
Science Policy
Skills
Software
Species richness
Taxa
Taxonomy
User interface
User-Computer Interface
Web Browser
Web site management software
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Description
Summary:Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0309707