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

Overview of Transposition and Recombination

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

Homologous Recombination

Homologous Recombination

Homologous Recombination

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...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

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:

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

You might also read

Related Articles

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

Sort by

Same author

An explainable machine learning framework for computable physiologic risk representation in preanesthetic assessment: Development and external validation.

International journal of medical informatics·2026

Same author

Terminally Differentiated Influenza-Specific Effector Memory B Cells Circulate after Live Attenuated Influenza Vaccination.

bioRxiv : the preprint server for biology·2026

Same author

A single-cell cytokine dictionary of human peripheral blood.

Research square·2026

Same author

Conventional versus pump-controlled retrograde trial off (PCRTO) weaning in V-A ECMO: exploring feasibility, physiological insights and benefits.

Critical care (London, England)·2025

Same author

Age- and ApoE Genotype-Dependent Transcriptomic Responses to O<sub>3</sub> in the Hippocampus of Mice.

International journal of molecular sciences·2025

Same author

Mechanical life support algorithm for the emergency management of patients with left-sided Impella.

The British journal of cardiology·2024

Search research articles

Related Experiment Video

Updated: Apr 11, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Comprehensive characterization of V(D)J recombination from long-read transcriptomic data with VDJcraft.

Kaili Hu¹, Alexander Rosenberg¹, Yuwei Song¹

¹Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.

Biorxiv : the Preprint Server for Biology

|April 10, 2026

Summary

VDJcraft is a new pipeline for analyzing V(D)J recombination in long-read sequencing data. It accurately identifies immune receptor genes and aids in discovering disease-associated immune signatures.

Keywords:

V(D)J recombination VDJcraft application immune long-read sequencing novel performance pipeline

More Related Videos

Recombineering Homologous Recombination Constructs in Drosophila

Recombineering Homologous Recombination Constructs in Drosophila

Published on: July 13, 2013

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Published on: February 3, 2013

Related Experiment Videos

Last Updated: Apr 11, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Recombineering Homologous Recombination Constructs in Drosophila

Recombineering Homologous Recombination Constructs in Drosophila

Published on: July 13, 2013

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Published on: February 3, 2013

Area of Science:

Immunology
Genomics
Bioinformatics

Background:

V(D)J recombination is crucial for generating antigen receptor diversity in developing B and T cells.
Long-read transcriptome sequencing offers higher accuracy for V(D)J event resolution compared to short-read methods.
Existing analysis tools are not optimized for long-read data.

Purpose of the Study:

To develop the first integrated pipeline, VDJcraft, for V(D)J recombination analysis using long-read transcriptome sequencing data.
To improve the accuracy and sensitivity of V(D)J gene detection and recombination analysis.

Main Methods:

VDJcraft employs a two-pass alignment strategy: global alignment with minimap2 and local realignment with IMGT.
A customized module enhances D-gene detection sensitivity and positional precision.
Consensus-based correction reduces sequencing errors, and IMGT motifs annotate antigen-binding regions.

Main Results:

VDJcraft accurately recovered full-length V(D)J-C sequences, outperforming existing methods in gene detection and accuracy.
Long-read VDJ calls showed significantly higher concordance with high-confidence short-read calls.
Identified 31 novel gene subclasses and revealed distinct V(D)J recombination patterns in a COVID-19 patient.

Conclusions:

VDJcraft provides a robust framework for V(D)J characterization using long-read sequencing.
The pipeline enables the discovery of disease-associated immune signatures and novel immune gene subclasses.