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...

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...

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....

DNA Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

You might also read

Related Articles

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

Sort by

Same author

High-resolution metagenome assembly for modern long reads with myloasm.

Nature biotechnology·2026

Same author

Simple and Thorough Detection of Related Sequences with Position-Varying Probabilities of Substitutions, Insertions, and Deletions.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same author

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.

bioRxiv : the preprint server for biology·2025

Same author

Long-read reconstruction of many diverse haplotypes with devider.

Genome research·2025

Same author

High-resolution metagenome assembly for modern long reads with myloasm.

bioRxiv : the preprint server for biology·2025

Same author

The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.

Journal of computational biology : a journal of computational molecular cell biology·2024

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026

Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026

Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026

Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026

Same journal

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

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 12, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

How to optimally sample a sequence for rapid analysis.

Martin C Frith^1,2,3, Jim Shaw⁴, John L Spouge⁵

¹Artificial Intelligence Research Center, AIST, Tokyo 135-0064, Japan.

Bioinformatics (Oxford, England)

|January 26, 2023

Summary

This summary is machine-generated.

A new sequence-sampling method optimizes genetic data analysis for speed and accuracy. This approach improves upon existing techniques, offering better sensitivity and specificity for diverse biological sequence comparisons.

More Related Videos

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Published on: March 30, 2014

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Related Experiment Videos

Last Updated: Aug 12, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Published on: March 30, 2014

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Area of Science:

Computational biology
Bioinformatics
Genomics

Background:

Increasing volume of genetic sequence data necessitates efficient computational analysis.
Current sequence-sampling methods (e.g., minimizers, syncmers) are heuristic and suboptimal.
Rapid analysis requires sampling sequence positions, but existing methods lack provable optimality.

Purpose of the Study:

To develop a novel, provably optimal sequence-sampling approach for genetic data.
To enhance the accuracy and efficiency of sequence comparison methods.
To improve specificity in biological DNA analysis by avoiding simple repeats.

Main Methods:

Developed a sequence-sampling method with provable sensitivity optimization for random sequences.
Generalized concepts of universal hitting sets and polar sets for sequence sampling.
Evaluated performance for alignment-based and alignment-free analyses.

Main Results:

The new method offers provable sensitivity optimization for a class of sequence comparison methods.
Demonstrated near-optimal performance for various alignment-based and alignment-free analyses.
Increased specificity for real biological DNA by effectively avoiding simple repeats.

Conclusions:

The presented sequence-sampling approach significantly advances rapid and accurate genetic data analysis.
This method provides a more robust and efficient alternative to existing heuristic techniques.
The approach offers a deeper understanding of optimizing sequence analysis for biological applications.