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

Genome Copying Errors02:46

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.
Detection of Gross Error: The Q Test01:00

Detection of Gross Error: The Q Test

When one or more data points appear far from the rest of the data, there is a need to determine whether they are outliers and whether they should be eliminated from the data set to ensure an accurate representation of the measured value. In many cases, outliers arise from gross errors (or human errors) and do not accurately reflect the underlying phenomenon. In some cases, however, these apparent outliers reflect true phenomenological differences. In these cases, we can use statistical methods...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

Overview
Mismatch Repair01:36

Mismatch Repair

Overview
Proofreading01:43

Proofreading

Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA strand. DNA polymerase has a higher affinity for the correct base to ensure fidelity in DNA replication. The DNA polymerase furthermore proofreads during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.Errors during Replication Are Corrected by the DNA Polymerase EnzymeGenomic DNA is synthesized in...

You might also read

Related Articles

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

Sort by
Same author

An encyclopedia of human enhancer-gene regulatory interactions.

Nature·2026
Same author

Indirect genomic effects shape cancer risk across species.

bioRxiv : the preprint server for biology·2026
Same author

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

bioRxiv : the preprint server for biology·2026
Same author

Teaching an old dog new cells.

Nature methods·2026
Same author

Sequence design for three-dimensional genome folding using Akita Semifreddo.

bioRxiv : the preprint server for biology·2026
Same author

The Common Fund Data Ecosystem (CFDE).

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jun 6, 2026

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

Quake: quality-aware detection and correction of sequencing errors.

David R Kelley1, Michael C Schatz, Steven L Salzberg

  • 1Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA. dakelley@umiacs.umd.edu

Genome Biology
|December 1, 2010
PubMed
Summary

Quake is a new open-source software that accurately detects and corrects errors in DNA sequencing reads. This improves downstream applications like genome assembly and single nucleotide polymorphism detection.

More Related Videos

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

Related Experiment Videos

Last Updated: Jun 6, 2026

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

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DNA sequencing technologies generate vast amounts of data, but errors in sequencing reads can significantly impact downstream analyses.
  • Accurate error correction is crucial for reliable genomic research, including genome assembly and variant calling.

Purpose of the Study:

  • To introduce Quake, a novel software tool designed for the detection and correction of errors in DNA sequencing reads.
  • To evaluate the accuracy and performance of Quake using realistic simulated data.

Main Methods:

  • Quake employs a maximum likelihood approach for error correction.
  • The algorithm incorporates sequencing quality values and nucleotide-specific miscall rates to enhance accuracy.

Main Results:

  • Quake achieves the highest accuracy in correcting errors on realistically simulated DNA sequencing reads compared to existing methods.
  • Utilizing Quake for error correction leads to substantial improvements in de novo assembly and single nucleotide polymorphism (SNP) detection.

Conclusions:

  • Quake is a highly accurate and effective tool for DNA sequencing error correction.
  • The software demonstrates significant utility in improving critical genomic analyses, applicable to projects of all scales, including large human datasets.