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 microarray-based...

Maxam-Gilbert Sequencing

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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...

You might also read

Related Articles

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

Sort by

Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026

Same author

Genome-wide spectrum of coding DNA variations in Indian patients with amyotrophic lateral sclerosis.

Journal of neurology·2026

Same author

HOROSCOPE: Decoding human centromere architecture from short reads using <i>k</i>-mer signatures.

bioRxiv : the preprint server for biology·2026

Same author

Faroese whole genomes provide insight into ancestry and recent selection.

eLife·2026

Same author

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.

bioRxiv : the preprint server for biology·2026

Same author

A complete human pancreatic cancer genome.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Jun 25, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Tobias Rausch¹, Sergey Koren, Gennady Denisov

¹International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr. 63-73, Algorithmische Bioinformatik, Institut für Informatik, Takustr. 9, 14195 Berlin, Germany. rausch@inf.fu-berlin.de

Bioinformatics (Oxford, England)

|March 10, 2009

Summary

A new consensus tool addresses challenges in high-throughput sequencing by improving multi-read alignment for genome assembly and variation analysis. This algorithm enhances accuracy on simulated data, outperforming existing methods for complex sequencing tasks.

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

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Related Experiment Videos

Last Updated: Jun 25, 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

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput sequencing generates massive short-read data, presenting algorithmic challenges.
Accurate multi-read alignment is crucial for genome assembly, variation analysis, and insert sequencing.
A robust and versatile consensus tool is needed to handle these data complexities.

Purpose of the Study:

To present a novel multi-read alignment algorithm for de novo and reference-guided genome assembly.
To develop a consensus tool capable of handling large-scale, high-coverage sequencing data.

Main Methods:

The algorithm identifies shared segments across multiple reads.
It aligns these segments using a consistency-enhanced alignment graph.
The tool can be used stand-alone or integrated with the Celera Assembler.

Main Results:

The program demonstrates comparable quality to existing tools on real de novo sequencing data from the NCBI Short Read Archive.
On simulated datasets for insert sequencing and variation analyses, the developed program shows superior performance compared to other tools.
The algorithm effectively handles complex datasets, improving alignment accuracy.

Conclusions:

The presented consensus tool offers a robust solution for multi-read alignment in the era of high-throughput sequencing.
Its performance on challenging simulated data suggests significant utility for variation analyses and genome assembly.
The tool is available for download and integration, supporting diverse bioinformatics workflows.