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

Genomics02:02

Genomics

35.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.4K
RNA-seq03:21

RNA-seq

9.3K
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...
9.3K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

833
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
833
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

5.9K
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...
5.9K
Next-generation Sequencing03:00

Next-generation Sequencing

87.7K
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....
87.7K
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

42.4K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
42.4K

You might also read

Related Articles

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

Sort by
Same author

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage.

Nature communications·2026
Same author

Catalytic Enantioselective Dearomatizing [2,3]-Wittig Rearrangements Allow Divergent [2,3]-, [1,2]-, and Sommelet-Hauser-Type Products.

Journal of the American Chemical Society·2026
Same author

The acylative kinetic resolution of 1,2-azaborine naphthols.

Chemical science·2026
Same author

The catalytic enantioselective [1,2]-Wittig rearrangement cascade of allylic ethers.

Nature chemistry·2026
Same author

Effectiveness of Infliximab for Refractory Nonischemic Cerebral Enhancing Foreign-Body Granulomatous Lesions After Endovascular Therapy.

Neurology·2025
Same author

From Oxygen to Tellurium: The Impact of the Chalcogen on Nucleophilicities and Basicities of Isochalcogenourea Catalysts.

Angewandte Chemie (International ed. in English)·2025
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Apr 27, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

85.8K

The Amordad database engine for metagenomics.

Ehsan Behnam1, Andrew D Smith1

  • 1Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

Bioinformatics (Oxford, England)
|June 30, 2014
PubMed
Summary
This summary is machine-generated.

Amordad is a new database engine for alignment-free, content-based indexing of metagenomic datasets. It enables efficient identification of similar metagenomes at scale using geometric methods and nearest neighbor graphs.

More Related Videos

Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

694
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.7K

Related Experiment Videos

Last Updated: Apr 27, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

85.8K
Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

694
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.7K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Metagenomic data analysis faces significant challenges in sequence assembly and taxonomic unit identification.
  • Traditional methods are limited by species variation and horizontal gene transfer.
  • Large-scale metagenomic data organization is computationally intensive.

Purpose of the Study:

  • To introduce Amordad, a novel database engine for metagenomic data analysis.
  • To enable efficient, content-based indexing and comparison of large metagenomic datasets.
  • To overcome computational limitations in metagenomic data organization.

Main Methods:

  • Amordad employs an alignment-free, content-based indexing strategy.
  • It utilizes a geometric framework combining random hashing and nearest neighbor graphs.
  • The database refines over time through the application of random hash functions.

Main Results:

  • Amordad supports logarithmic query time for identifying similar metagenomes.
  • The engine scales efficiently, handling databases with millions of metagenomes.
  • Performance was validated on both real and simulated metagenomic datasets.

Conclusions:

  • Amordad offers a scalable and efficient solution for metagenomic data analysis.
  • The alignment-free, geometric approach overcomes limitations of traditional methods.
  • This engine facilitates large-scale content-based organization and comparison of metagenomic data.