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

Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.4K
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...
11.4K
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

12.8K
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
12.8K
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

801
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
801
Improving Translational Accuracy02:07

Improving Translational Accuracy

11.8K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.8K
Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

7.2K
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:
7.2K
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

54.1K
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...
54.1K

You might also read

Related Articles

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

Sort by
Same author

Analysis of Prognostic Significance of CD47 Expression in Newly Diagnosed Large B Cell Lymphoma.

Life (Basel, Switzerland)·2026
Same author

Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides targeting avian pathogenic Escherichia coli in broiler chickens.

Journal of animal science and biotechnology·2026
Same author

AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.

PLoS computational biology·2026
Same author

ntStat: k-mer characterization using occurrence statistics in raw sequencing data.

PLoS computational biology·2026
Same author

Varicella-Zoster Virus Infection in an Immunocompromised Patient With Seizure-Like Activity and Septic Shock: A Case Report.

Cureus·2026
Same author

AMPSeek: A Workflow for Predicting Antimicrobial Peptide Activity, Three-Dimensional Structure, and Toxicity.

Current protocols·2026
Same journal

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

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Sep 7, 2025

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

5.9K

RResolver: efficient short-read repeat resolution within ABySS.

Vladimir Nikolić1,2, Amirhossein Afshinfard1,2, Justin Chu1,2

  • 1Canada's Michael Smith Genome Sciences Centre at BC Cancer, 570 W 7th Ave, Vancouver, V5Z 4S6, Canada.

BMC Bioinformatics
|June 21, 2022
PubMed
Summary
This summary is machine-generated.

RResolver is a new scalable algorithm for de novo genome assembly that improves contiguity and reduces misassemblies. It efficiently resolves repeats in de Bruijn graphs, enhancing genomic analysis for complex genomes.

Keywords:
Bloom filtersDe novo assemblyRepeat resolutionScalableShort reads

More Related Videos

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.0K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

10.7K

Related Experiment Videos

Last Updated: Sep 7, 2025

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

5.9K
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

23.0K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

10.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • De novo genome assembly is crucial for genomics, especially for highly variable genomes like cancer.
  • De novo assemblers commonly use de Bruijn graphs, with k-mer size selection posing a trade-off between connectivity and contiguity.
  • Existing multi-k approaches struggle with scalability for large genomes.

Purpose of the Study:

  • To present RResolver, a scalable algorithm designed to resolve repeats in de novo genome assembly.
  • To improve the efficiency and accuracy of de Bruijn graph-based genome assembly.

Main Methods:

  • RResolver takes a de Bruijn graph assembly and a starting k-mer size as input.
  • It utilizes a Bloom filter of sequencing reads to assess path support at branching points.
  • Paths with insufficient support are removed to resolve repeats.

Main Results:

  • RResolver efficiently resolves repeats, completing an ABySS human assembly in 26 minutes with 48 threads.
  • It improves scaffold contiguity (NGA50) by up to 15% compared to baseline assemblies.
  • Misassemblies are reduced by up to 12%.

Conclusions:

  • RResolver addresses a gap in scalable de Bruijn graph genome assembly.
  • It enhances downstream ABySS algorithms by providing a more accurate and less complex genome representation.
  • The RResolver code is integrated into ABySS and publicly available.