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

Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
Sanger Sequencing01:57

Sanger Sequencing

771.0K
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...
771.0K
RNA-seq03:21

RNA-seq

11.5K
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...
11.5K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

12.3K
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...
12.3K
Next-generation Sequencing03:00

Next-generation Sequencing

97.1K
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....
97.1K

You might also read

Related Articles

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

Sort by
Same author

Double vs. single autologous stem cell transplantation in patients with multiple myeloma and high-risk factors: A systematic review and meta-analysis.

Oncology letters·2026
Same author

LUMINEX technology detects plasma inflammatory factor expression levels in children with severe and non-severe community acquired pneumonia.

BMC pediatrics·2026
Same author

Diffusion-enhanced Fine-grained Cross Semantic Fusion for Drug-disease Association Prediction.

IEEE journal of biomedical and health informatics·2026
Same author

Diagnostic value of unilateral adrenal vein sampling with simple and biochemical/imaging correction: a study on early screening and typing for primary aldosteronism.

BMC endocrine disorders·2026
Same author

Bisphenols, nonylphenols, and nonylphenol metabolites in paired dust and urine across China: insights into systemic oxidative stress.

Environment international·2026
Same author

APOE4 exacerbates glucocorticoid stress hormone-induced tau pathology via mitochondrial dysfunction.

Cell death & disease·2026
Same journal

Research on multi-trait genome association study method based on Shannon information entropy.

BMC bioinformatics·2026
Same journal

A multi-view feature fusion framework with interpretable graph convolution for predicting microbe-drug associations.

BMC bioinformatics·2026
Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Dec 14, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.4K

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles.

Zhenhua Yu1, Fang Du2, Rongjun Ban3

  • 1School of Information Engineering, Ningxia University, Yinchuan, 750021, China. zhyu@nxu.edu.cn.

BMC Bioinformatics
|July 25, 2020
PubMed
Summary
This summary is machine-generated.

SimuSCoP is a new bioinformatics tool that reliably emulates complex DNA sequencing data by fully exploring base substitution patterns and quality score behaviors. This efficient tool improves upon existing simulators for next-generation sequencing data analysis.

Keywords:
Base substitution errorsIntra-tumor heterogeneityNext-generation sequencingPhred base qualitySimulators

More Related Videos

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.6K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.4K

Related Experiment Videos

Last Updated: Dec 14, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.4K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.6K
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

34.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Existing next-generation sequencing simulators have functional and runtime limitations.
  • Positional and genomic contextual information is underutilized for base substitution patterns.
  • Phred quality score differences are not fully investigated in current simulation tools.

Purpose of the Study:

  • To develop a novel, effective, and efficient bioinformatics tool for reliable DNA sequencing data emulation.
  • To address the limitations of existing simulators in capturing complex sequencing data characteristics.

Main Methods:

  • Developed SimuSCoP, a novel tool for emulating complex DNA sequencing data.
  • Integrated comprehensive exploration of base substitution patterns and quality score statistical behavior.
  • Implemented an integrated, easy-to-use pipeline with multithreading for high runtime efficiency and low memory consumption.

Main Results:

  • SimuSCoP demonstrates substantial improvements in reliability, functionality, practicality, and runtime efficiency.
  • The tool accurately simulates genomic variations and complex tumor samples.
  • Evaluations show SimuSCoP outperforms existing simulation tools in consistency and profile simulation.

Conclusions:

  • SimuSCoP learns informative profiles from real sequencing data to reliably mimic complex data with genomic variations.
  • This new tool is expected to catalyze advancements in downstream bioinformatics methods for sequencing data analysis.