Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Sanger Sequencing01:57

Sanger Sequencing

765.4K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
765.4K
RNA-seq03:21

RNA-seq

10.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.9K
Next-generation Sequencing03:00

Next-generation Sequencing

95.5K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
95.5K
DNA Microarrays02:34

DNA Microarrays

19.5K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
19.5K
DNA Isolation01:34

DNA Isolation

196.1K
DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.
196.1K
DNA Isolation01:24

DNA Isolation

43.2K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
43.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Constructing a lower-bound estimate of the global number of insect species on a hyperdiverse empirical foundation.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Peat-based soil amendments enhance long-term soil-plant-microbe recovery in boreal mine reclamation.

Journal of environmental management·2026
Same author

How can biological databases support the new UN mechanism for benefit-sharing from digital sequence information?

Scientific data·2026
Same author

Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.

Genome biology and evolution·2026
Same author

Barcoding Megadiversity: An Arthropod Database from Sites in the Neotropical Eastern Pacific Bioregion.

Scientific data·2026
Same author

Towards a Complete DNA Barcode Library of Austrian Lepidoptera.

Insects·2026
Same journal

From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.

Molecular ecology resources·2026
Same journal

EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.

Molecular ecology resources·2026
Same journal

A Practical Framework for GT-Seq Panel Optimization.

Molecular ecology resources·2026
Same journal

Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.

Molecular ecology resources·2026
Same journal

pr2-Wormifier: A Bioinformatics Pipeline to Create Custom Reference Databases for Improved Metabarcoding of Marine Protists.

Molecular ecology resources·2026
Same journal

Individual Identification of Prey in Carnivore Scats.

Molecular ecology resources·2026
See all related articles

Related Experiment Video

Updated: Nov 12, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

14.2K

Debar: A sequence-by-sequence denoiser for COI-5P DNA barcode data.

Cameron M Nugent1,2, Tyler A Elliott2, Sujeevan Ratnasingham2

  • 1Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.

Molecular Ecology Resources
|March 22, 2021
PubMed
Summary
This summary is machine-generated.

A new R package, debar, effectively removes instrument errors from DNA barcode sequences. This tool enhances biodiversity assessments by improving the accuracy of species identification using the COI gene.

Keywords:
COIDNA barcodeMarkov modelbiodiversitydenoisingmetabarcode

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.3K
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

3.9K

Related Experiment Videos

Last Updated: Nov 12, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

14.2K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.3K
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
06:24

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

3.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Ecology

Background:

  • DNA barcoding and metabarcoding are crucial for species discovery and biodiversity studies.
  • High-throughput sequencing (HTS) increases data but introduces technical errors, inflating biodiversity estimates.
  • Current denoising methods for barcode data do not leverage the conserved structure of the cytochrome c oxidase subunit I (COI) gene.

Purpose of the Study:

  • To introduce debar, an R package designed to denoise indel errors in animal COI sequences.
  • To improve the accuracy of DNA barcode and metabarcode data by separating biological signal from technical noise.
  • To enhance species diversity characterization through more reliable sequence data.

Main Methods:

  • Development of debar, an R package utilizing a profile hidden Markov model.
  • Application of debar to denoise indel errors in COI sequences generated by HTS.
  • In silico and real-world data validation of debar's performance on different sequencing platforms.

Main Results:

  • Debar successfully recognized 95% of artificial indels in silico COI sequences.
  • Debar reduced indel errors by 75% in circular consensus sequences from the Sequel platform.
  • Debar achieved a 94% reduction in indel errors for sequences from the Ion Torrent S5 platform, with a false correction rate below 0.1%.

Conclusions:

  • The debar package significantly improves DNA barcoding and metabarcoding workflows.
  • Debar facilitates the generation of more accurate COI sequences, aiding precise species diversity characterization.
  • This tool enhances the reliability of biodiversity assessments by minimizing technical noise in sequence data.