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

Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...

Long-patch Base Excision Repair

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:

Mismatch Repair

Mismatch Repair

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

You might also read

Related Articles

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

Sort by

Same author

A Robust Deep Learning Approach for Position-Independent Smartphone-Based Human Activity Recognition.

Sensors (Basel, Switzerland)·2018

See all related articles

Search research articles

Related Experiment Video

Updated: Sep 5, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Fast-HBR: Fast hash based duplicate read remover.

Sami Altayyar¹, Abdel Monim Artoli¹

¹Department of Computer Science, College of Computer and Information Sciences, King Saud University, P.O. Box 51178, Riyadh 11543, Saudi Arabia.

|July 11, 2022

Summary

Fast-HBR efficiently removes duplicate reads from Next-Generation Sequencing data without a reference genome. This tool enhances data analysis accuracy and speed for environmental samples.

Area of Science:

Bioinformatics
Genomics
Environmental Science

Background:

Next-Generation Sequencing (NGS) generates vast datasets for environmental sample analysis.
Duplicate reads within NGS data reduce analytical efficiency and accuracy.
Existing de-novo duplicate removal tools can be resource-intensive.

Purpose of the Study:

To introduce Fast-HBR, a novel tool for efficient duplicate read removal in NGS data.
To provide a de-novo approach for duplicate removal, eliminating the need for a reference genome.
To improve the speed and memory efficiency of duplicate read processing.

Main Methods:

Fast-HBR utilizes hash tables to represent sequencing reads as integers, minimizing memory footprint.
The tool operates on de-novo principles, processing reads without relying on a reference genome.

More Related Videos

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Related Experiment Videos

Last Updated: Sep 5, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Implementation in Python 3 ensures accessibility and ease of use.

Main Results:

Fast-HBR demonstrates superior speed compared to existing de-novo duplicate removal tools.
The tool exhibits a significantly lower memory footprint, enhancing computational efficiency.
Effective removal of duplicate reads improves the quality of downstream environmental data analysis.

Conclusions:

Fast-HBR offers a fast and memory-efficient solution for de-novo duplicate read removal in NGS data.
The tool is particularly valuable for analyzing environmental samples where reference genomes may be unavailable or impractical.
Fast-HBR contributes to more accurate and efficient genomic data analysis workflows.