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

PCR - Polymerase Chain Reaction01:32

PCR - Polymerase Chain Reaction

Overview
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
RNA-seq03:21

RNA-seq

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 microarray-based...
¹H NMR Signal Multiplicity: Splitting Patterns01:13

¹H NMR Signal Multiplicity: Splitting Patterns

When protons A and X are coupled, their nuclear spin energy levels are slightly modified. This is because the energy required to excite proton A to a spin state parallel to proton X is slightly different from the energy required for it to become anti-parallel to spin X. Consequently, there are two possible excitation frequencies for A (A1 and A2), depending on the spin state of X, and vice versa. The mutual nature of coupling implies that the difference between frequencies A1 and A2, indicated...
Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...
Encoding01:19

Encoding

Information enters the brain through encoding, which is the input of information into the memory system. Once sensory information is received from the environment, the brain labels or codes it. The information is then organized with similar information and connected to existing concepts. Encoding occurs through automatic processing and effortful processing.
Automatic processing involves the encoding of details like time, space, frequency, and the meaning of words, usually done without conscious...

You might also read

Related Articles

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

Sort by
Same author

Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for dalbergioid-rhizobium symbiosis.

BMC plant biology·2026
Same author

Assembling telomere-to-telomere genomes of Fusarium oxysporum f. sp. lactucae provides a roadmap for studying genome and phenotype evolution.

BMC genomics·2026
Same author

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid.

ACS synthetic biology·2026
Same author

Cryptostroma corticale, a plant pathogen associated with a human immune respiratory syndrome displaying mixed viral infections of mycoviruses.

Virology·2026
Same author

PAQman: reference-free ensemble evaluation of long-read genome assemblies.

G3 (Bethesda, Md.)·2026
Same author

The poplar pathogen <i>Sphaerulina musiva</i> has a dynamic genome architecture marked by chromosomal inversions and changes in transposable element abundance.

Microbial genomics·2026

Related Experiment Video

Updated: May 12, 2026

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
08:30

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

14.1K

Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes.

Martha A Sudermann1, Zachary S L Foster2, Samantha C L Dawson1

  • 1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.

Phytopathology
|April 25, 2025
PubMed
Summary

Demulticoder is a new R package that automates the analysis of multiple DNA metabarcodes, simplifying complex community identification. This tool significantly reduces manual steps, ensuring comparable data quality to standard workflows.

Keywords:
bioinformaticscomputational biologyecologymicrobiomeoomycetestechniques

More Related Videos

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

4.3K
Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

2.3K

Related Experiment Videos

Last Updated: May 12, 2026

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
08:30

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

14.1K
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

4.3K
Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
08:18

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

2.3K

Area of Science:

  • Ecology
  • Bioinformatics
  • Molecular Biology

Background:

  • Metabarcoding uses DNA sequences to identify organisms in communities.
  • Existing workflows are inefficient for multiple or novel metabarcodes, especially for diverse taxa like soil microbes.
  • Analyzing diverse taxa often requires multiple metabarcodes, increasing workflow complexity.

Purpose of the Study:

  • To develop demulticoder, an R package automating DADA2 analysis for multiple metabarcodes.
  • To streamline metabarcoding data processing, reducing manual input and enabling automated analysis of multiplexed data.
  • To provide a versatile tool for analyzing single, multiplexed, or pooled metabarcodes.

Main Methods:

  • Developed the demulticoder R package for automated metabarcoding analysis.
  • Integrated DADA2 for sequence variant identification.
  • Updated the oomycete rps10 barcode database with revised taxonomic information.
  • Compared demulticoder to a standard workflow using a multiplexed ITS1 and rps10 dataset.

Main Results:

  • Demulticoder reduced manual input steps from 28 to 4 compared to standard workflows.
  • Data quality and downstream analysis results (exploratory, diversity, differential abundance) were comparable.
  • The oomycete rps10 database was updated for improved taxonomic accuracy.
  • Demulticoder successfully analyzed multiplexed ITS1 and rps10 metabarcodes.

Conclusions:

  • Demulticoder simplifies and automates multi-metabarcoding data analysis.
  • The package offers a versatile, efficient, and user-friendly alternative to standard workflows.
  • Demulticoder ensures high data quality and is suitable for diverse metabarcoding applications.