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

Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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...

You might also read

Related Articles

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

Sort by
Same author

Cytoplasmic and nuclear extracellular signal-regulated kinases are necessary for <i>Campylobacter jejuni</i> infection.

Frontiers in microbiology·2026
Same author

Campylobacter jejuni regulates cell cycle progression to potentiate host cell invasion.

Cell communication and signaling : CCS·2025
Same author

Circulating trimethylamine N-oxide and cardiovascular, cerebral, and renal diseases including mortality: Umbrella review of published systematic reviews and meta-analyses.

Nutrition, metabolism, and cardiovascular diseases : NMCD·2025
Same author

Towards an Evolutionary Model of Animal-Associated Microbiomes.

Entropy (Basel, Switzerland)·2025
Same author

Correction to: Genetic Risk, Dysbiosis, and Treatment Stratification Using Host Genome and Gut Microbiome in Inflammatory Bowel Disease.

Clinical and translational gastroenterology·2024
Same author

Single-cell multiomics reveal divergent effects of DNMT3A- and TET2-mutant clonal hematopoiesis in inflammatory response.

Blood advances·2024
Same journal

Thymidylate synthase inhibitory drugs induce p53-dependent pathways differently.

PloS one·2026
Same journal

Top-down and bottom-up attention for joint pattern classification and reconstruction.

PloS one·2026
Same journal

Short- and long-term scaling behavior of blood pressure and pulse arrival time during sleep in healthy controls and patients with obstructive sleep apnea.

PloS one·2026
Same journal

Double DQN-based secrecy energy efficiency and fairness performance in IRS-assisted NOMA systems with friendly jamming.

PloS one·2026
Same journal

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century.

PloS one·2026
Same journal

Paying in public: Peer effects, impression management, and willingness to pay on digital payment platforms.

PloS one·2026
See all related articles

Related Experiment Video

Updated: Jun 5, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Robust computational analysis of rRNA hypervariable tag datasets.

Maksim Sipos1, Patricio Jeraldo, Nicholas Chia

  • 1Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

Plos One
|January 11, 2011
PubMed
Summary
This summary is machine-generated.

Next-generation DNA sequencing of microbial communities can be prone to errors. This study quantifies alignment and clustering errors, offering procedural optimizations for accurate abundance and diversity estimation in 16S rRNA datasets.

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

Related Experiment Videos

Last Updated: Jun 5, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)
09:26

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing (RIPiT-Seq)

Published on: July 10, 2019

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Next-generation DNA sequencing is crucial for analyzing microbial communities, particularly the gastrointestinal microbiome.
  • Accurate quantification of microbial abundance and diversity is essential for these analyses.
  • 16S rRNA gene sequencing datasets are large and fragmented, susceptible to experimental and computational artifacts.

Purpose of the Study:

  • To quantify the impact of multiple alignment and clustering errors on abundance and diversity estimates.
  • To identify procedural optimizations for handling large 16S rRNA datasets.
  • To introduce metrics for assessing the quality of microbial community analysis estimators.

Main Methods:

  • Quantification of errors from multiple alignment and clustering in 16S rRNA datasets.
  • Implementation of procedural optimizations using existing bioinformatics tools.
  • Development and application of metrics to evaluate clustering quality for pyrosequenced rRNA data.

Main Results:

  • Alignment and clustering errors lead to overestimation of microbial abundance and diversity.
  • Errors result in incorrect operational taxonomic unit (OTU) assignment and corrupted phylogenies.
  • Complete linkage clustering demonstrates superior performance compared to other methods for rRNA data.

Conclusions:

  • Procedural optimizations effectively mitigate errors in large 16S rRNA datasets.
  • New metrics aid in assessing the quality of microbial diversity and abundance estimations.
  • Complete linkage clustering is recommended for improved accuracy in pyrosequenced rRNA data analysis.