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

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.

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...

Next-generation Sequencing

Next-generation Sequencing

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....

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

Protein Complex Assembly

Protein Complex Assembly

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

You might also read

Related Articles

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

Sort by

Same author

Para infectious myelitis with Conus medullaris immunotropism in the immune phase of leptospirosis infection: Clinical pattern and in silico molecular mimicry analysis based biological plausibility.

Journal of neuroimmunology·2026

Same author

Improved reference assembly and core collection resequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius L.

GigaScience·2025

Same author

Epigenetic modulation rescues neurodevelopmental deficits in Syngap1<sup>+/-</sup> mice.

Aging cell·2025

Same author

Global proteomics reveals pathways of mesenchymal stem cells altered by Mycobacterium tuberculosis.

Scientific reports·2024

Same author

ACSL4-mediated H3K9 and H3K27 hyperacetylation upregulates SNAIL to drive TNBC metastasis.

Proceedings of the National Academy of Sciences of the United States of America·2024

Same author

Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy.

The Biochemical journal·2024

Search research articles

Related Experiment Video

Updated: Mar 31, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler.

Kiran Gopinath Bankar¹, Vivek Nagaraj Todur¹, Rohit Nandan Shukla¹

¹Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bangalore 560043, India.

|October 21, 2015

Summary

Next Generation Sequencing enables de novo transcriptome assembly without a genome. This study presents an improved method using Illumina reads and Trinity Assembler for enhanced transcriptome data quality.

Keywords:

De novo transcriptome assembly Illumina Trinity

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Related Experiment Videos

Last Updated: Mar 31, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Bioinformatics
Genomics
Transcriptomics

Background:

Next Generation Sequencing (NGS) allows de novo transcriptome assembly for organisms lacking a reference genome.
Illumina sequencing is a prevalent platform due to its data quality, quantity, and cost-effectiveness.
Several de novo transcriptome assemblers are available for constructing transcriptomes.

Purpose of the Study:

To achieve an ameliorated de novo transcriptome assembly using Illumina sequencing reads.
To evaluate and improve transcriptome assembly generated by the Trinity Assembler.

Main Methods:

Utilized sequence reads from the Illumina platform.
Employed the Trinity Assembler for the initial de novo transcriptome assembly.
Developed an amelioration approach based on transcript length, coverage, depth, and protein homology.

Main Results:

The primary Trinity assembly was successfully ameliorated.
The amelioration process improved key metrics including transcript length, coverage, and depth.
Protein homology was used as a criterion for refining the assembly.

Conclusions:

The proposed amelioration approach is reproducible.
This method enhances the sensitivity and specificity of the assembled transcriptome.
Improved transcriptome assembly is crucial for transcript validation and downstream biological assays.