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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
RNA-seq03:21

RNA-seq

9.8K
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...
9.8K

You might also read

Related Articles

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

Sort by
Same author

CYP3A-Mediated Metabolism of Zastaprazan in Humans and Associated Drug-Drug Interactions.

Pharmaceutics·2026
Same author

Transformation and transport: Polyvinyl chloride microplastics modulate fipronil accumulation and toxicity in zebrafish.

Journal of environmental sciences (China)·2026
Same author

Pharmacokinetics, mass balance, and metabolism of the novel potassium-competitive acid blocker JP-1366 in healthy Chinese adults following a single oral dose of [<sup>14</sup>C]JP-1366.

Frontiers in pharmacology·2025
Same author

Personalized Federated Learning Based on Dynamic Parameter Fusion and Prototype Alignment.

Sensors (Basel, Switzerland)·2025
Same author

Prediction of drug concentrations in humans for long-acting injectable suspensions by a semi-mechanical muscle compartment model: a case study of paliperidone palmitate.

Frontiers in pharmacology·2025
Same author

Smartphone-assisted colorimetric sensing hydrogels based on MnO<sub>2</sub> NFs nanozyme for highly sensitive and rapid detection of tert-butylhydroquinone in edible oils.

Food chemistry·2025

Related Experiment Video

Updated: Jun 9, 2025

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.7K

Binning Metagenomic Contigs Using Contig Embedding and Decomposed Tetranucleotide Frequency.

Long Fu1, Jiabin Shi1, Baohua Huang1,2

  • 1School of Computer and Electronic Information, Guangxi University, Nanning 530004, China.

Biology
|October 25, 2024
PubMed
Summary

CedtBin improves metagenomic binning by integrating contig embeddings and decomposed tetranucleotide frequencies. This novel approach enhances genome reconstruction accuracy for microbial species identification.

Keywords:
Approximate Nearest Neighbors Oh Yeah (Annoy)BERTDBSCAN algorithmbinningmetagenomicsnon-negative matrix factorization (NMF)tetranucleotide

More Related Videos

Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

8.6K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.5K

Related Experiment Videos

Last Updated: Jun 9, 2025

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.7K
Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

8.6K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Metagenomic binning is essential for assembling microbial genomes from complex samples.
  • Current binning methods often fail to fully utilize sequence information, leading to suboptimal results.
  • Existing techniques struggle with effective tetranucleotide frequency processing and semantic feature extraction.

Purpose of the Study:

  • To develop an advanced metagenomic binning method, CedtBin, that overcomes limitations of existing approaches.
  • To enhance the accuracy and efficiency of aggregating microbial genome sequences.
  • To improve the reconstruction of genomes from metagenomic data.

Main Methods:

  • Utilizing an improved BERT model for learning contig embeddings, capturing semantic information.
  • Decomposing tetranucleotide frequencies via Non-negative Matrix Factorization (NMF).
  • Integrating contig embeddings and decomposed frequencies for clustering, and introducing an adaptive Annoy-DBSCAN algorithm for parameter optimization.

Main Results:

  • CedtBin demonstrated superior binning performance compared to mainstream methods on both simulated and real datasets.
  • The method successfully reconstructed a greater number of genomes, indicating enhanced accuracy.
  • The adaptive Annoy-DBSCAN algorithm effectively addressed parameter sensitivity issues in DBSCAN.

Conclusions:

  • CedtBin offers a significant advancement in metagenomic binning by leveraging rich feature representations.
  • The proposed method provides a more effective and robust solution for microbial genome assembly.
  • CedtBin's ability to reconstruct more genomes highlights its practical utility in metagenomic research.