Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

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...

Ribosome Profiling

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...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Genomics

Genomics

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...

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

Genetic variants in the development of autoimmune complaints and capsular contracture in women with breast implants: A systematic review.

JPRAS open·2025

Same author

Silicone Breast Implants and Autoimmunity: A case report.

JPRAS open·2024

Same author

A case report of BIA-ALCL: Diagnostic, treatment, and mammary reconstruction.

International journal of surgery case reports·2024

Same author

Landscape of global urban environmental resistome and its association with local socioeconomic and medical status.

Science China. Life sciences·2024

Same author

Bioactive compounds as an alternative for the sugarcane industry: Towards an integrative approach.

Heliyon·2023

Same author

Systematic discrimination of the repetitive genome in proximity of ferroptosis genes and a novel prognostic signature correlating with the oncogenic lncRNA CRNDE in multiple myeloma.

Frontiers in oncology·2023

Search research articles

Related Experiment Video

Updated: May 12, 2026

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Exploration of noncoding sequences in metagenomes.

Fabián Tobar-Tosse¹, Adrián C Rodríguez, Patricia E Vélez

¹Colombian Center for Genomics and Bioinformatics of Extreme Environments Gebix, Bogota, Colombia.

|March 29, 2013

Summary

This study reveals that noncoding sequences in metagenomes contain crucial regulatory and adaptive information often missed by traditional ORF analysis. Incorporating these sequences enhances metagenome organization and environmental association.

More Related Videos

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: May 12, 2026

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Metagenomics
Genomics
Bioinformatics

Background:

Metagenome analysis commonly focuses on Open Reading Frames (ORFs), potentially overlooking valuable noncoding sequence information.
Environment-specific genomic features are linked to metagenomes, but ORF-centric methods may miss regulatory or structural insights.

Purpose of the Study:

To investigate the significance of noncoding sequences in metagenomes.
To analyze coding and noncoding sequences using genomic patterns like (G+C) content, Codon Usage, and Trinucleotide Usage.
To demonstrate the relevance of noncoding sequences for metagenome classification and environmental association.

Main Methods:

Analysis of 23 whole metagenomes, including both coding and noncoding sequences.
Utilized sequence patterns: (G+C) content, Codon Usage (Cd), and Trinucleotide Usage (Tn).
Functional assignments for ORF prediction were also incorporated.

Main Results:

A significant proportion of noncoding sequences are discarded in standard metagenomic analyses.
High density of trinucleotide repeat sequences (TRS) found in noncoding regions, suggesting regulatory and adaptive roles.
Associations were found between trinucleotide values, gene function, and metagenome clustering, correlating with microbial adaptations and metagenome types.

Conclusions:

Noncoding sequences harbor critical information for comprehensive metagenome analysis.
Including noncoding sequences can improve metagenome organization, classification, and understanding of environmental relationships.
Trinucleotide usage patterns in noncoding DNA offer insights into microbial adaptation and community structure.