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

Lagging Strand Synthesis01:59

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Sanger Sequencing01:57

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...
Long-patch Base Excision Repair01:02

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:
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...

You might also read

Related Articles

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

Sort by
Same author

Respiratory modulation of neurophysiology and symptoms in athletes with sports-related concussion: a randomized crossover trial.

Frontiers in neuroscience·2026
Same author

A Restricted Two-Stage Multi-Locus Multi-Allele Genome-Wide Association Study Reveals Genomic Loci and Candidate Genes Controlling Plant-Height-Related Traits in Soybean Under Normal and Shade Conditions.

International journal of molecular sciences·2026
Same author

Phospholipid remodeling interplays with auxin signaling to modulate cellular reprogramming in Arabidopsis regeneration.

The Plant cell·2026
Same author

Persona-based stratification and XGBoost modeling for multi-dimensional vehicle sound quality evaluation.

Scientific reports·2026
Same author

High-entropy alloys in a radial mesostructured TiO<sub>2</sub> support for efficient hydrogen evolution.

Materials horizons·2026
Same author

Intraperitoneal and Intravenous Paclitaxel Plus S-1 for Gastric Cancer With Peritoneal Metastasis: A Phase 3 Randomized Clinical Trial.

JAMA oncology·2026
Same journal

Model-based quantification of protein-protein interaction aberrations for exploring dysregulated signalling pathways through pathway maps and gene expression levels.

BMC bioinformatics·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
See all related articles

Related Experiment Video

Updated: Jun 25, 2026

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

Short read DNA fragment anchoring algorithm.

Wendi Wang1, Peiheng Zhang, Xinchun Liu

  • 1Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, PR China. wangwendi@ncic.ac.cn

BMC Bioinformatics
|February 12, 2009
PubMed
Summary
This summary is machine-generated.

The EMBF algorithm significantly accelerates the anchoring of short DNA fragments from next-generation sequencing. It offers substantial efficiency gains over existing tools like BLAT and SOAP for large-scale bioinformatics analysis.

More Related Videos

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

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

Related Experiment Videos

Last Updated: Jun 25, 2026

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

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

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) technologies accelerate genome sequencing and reduce costs.
  • NGS technologies produce short DNA fragments (30-50 bps), necessitating efficient anchoring to reference sequences.
  • Anchoring short fragments to large reference sequences presents a computational bottleneck in bioinformatics.

Purpose of the Study:

  • To develop and evaluate an efficient algorithm for anchoring short DNA fragments.
  • To address the computational challenges posed by the increasing volume of NGS data.

Main Methods:

  • Comparison of algorithm efficiency using BLAT, SOAP, and EMBF.
  • Efficiency is defined as the ratio of total output results to consumed time.
  • Evaluation was performed on large reference sequences.

Main Results:

  • The EMBF algorithm demonstrated 3-4 times greater efficiency than SOAP.
  • EMBF showed at least 150 times greater efficiency than BLAT.
  • EMBF performance remained stable with increasing reference sequence size, unlike SOAP which degraded by up to 30%.

Conclusions:

  • EMBF is highly suitable for anchoring short DNA fragments from NGS data.
  • The algorithm excels in scenarios requiring result completeness and accuracy with large reference sequences.
  • EMBF offers a significant computational advantage for large-scale genomic analysis.