相关实验视频

Updated: Sep 14, 2025

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

clonevdjseq:一个工作流和生物信息管理系统,用于对来自克隆库的VDJ序列进行测序,存档和分析

Keith Mitchell^1,2, Samuel Hunter³, Lutz Froenicke⁴

¹Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, USA. kgmitchell@ucdavis.edu.

BMC bioinformatics

|July 22, 2025

概括

clonevdjseq是一个新的生物信息学工具,用于分析来自大型数据集的B细胞和T细胞受体序列. 它为研究抗原识别和抗体开发的研究人员提供了灵活和可扩展的解决方案.

科学领域:

免疫学免疫学免疫学
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

下一代测序产生了大量的B细胞受体 (BCR) 和T细胞受体 (TCR) 序列数据.
现有的生物信息学工具在大型克隆数据集所需的规模和灵活性方面扎.
之前的混合体依赖代码缺乏广泛的系统兼容性.

研究的目的:

为BCR/TCR序列分析开发一个集成,可访问和可扩展的软件解决方案.
为了提高大型克隆数据集的灵活性和建模能力.
为更广泛的系统兼容性提供技术补充.

主要方法:

使用 Nextflow 和 Django 开发了 clonevdjseq.
集成模块用于读取处理,放大器消噪和质量控制.
基于高吞吐量库准备协议构建的.
包括可选的数据库和用于数据传播的网络应用程序.

主要成果:

clonevdjseq有效地处理大型杂交细胞库和同质细胞群.
管道模块可以处理配对的可变轻/重链 (BCR) 和α/β,delta/gamma链 (TCR).
处理的数据经过数千个单克隆抗体的验证,使得重组抗体的开发成为可能.
生成的序列为NeuroMabSeq倡议和其他建模应用做出了贡献.

结论:

clonevdjseq为VDJ数据集处理和分析提供了一个全面的,可扩展的解决方案.
模块化设计,动态管道和数据库集成确保了高效的数据管理.
公开可用的平台支持对混合体和单细胞群的BCR/TCR序列存档和传播.

关键词:

在BCR序列化中,BCR序列化生物信息学是一种生物信息学.一个克隆克隆.克洛尼夫德泽斯基克尔 (克洛尼夫德泽斯基克尔) 在数据库数据库数据库是一个数据库.达戈 (Django) 是一个多元化的语言.混合体瘤是一种混合体瘤.单克隆抗体是一种单克隆抗体.没有NGS,没有NGS.下一个流程下一个流程在Nf-核心.单细胞机是一种单细胞机.TCR 测序的测序方法 VDJJ是什么意思

更多相关视频

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

相关概念视频

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

Sanger Sequencing

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...

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...