Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
DNA as a Genetic Template02:05

DNA as a Genetic Template

21.6K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
21.6K
Phylogenetic Trees03:21

Phylogenetic Trees

45.1K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.1K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
Next-generation Sequencing03:00

Next-generation Sequencing

87.2K
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....
87.2K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

Quantitative Assessment of Brain Glucose Metabolism Using Dynamic Glucose-Enhanced Magnetic Resonance Fingerprinting (DGE-MRF).

Chemical & biomedical imaging·2026
Same author

Weak solutions to the Bloch equations with distant dipolar field.

The Journal of chemical physics·2026
Same author

Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish.

Nature aging·2026
Same author

Admissibility of solitary wave modes in long-runout debris flows.

Physical review. E·2025
Same author

Toward a formulation of a CISS theory with the inclusion of two-particle relativistic effects, electron-phonon coupling, and electron-electron correlation. An application to NMR-based chiral discrimination.

The Journal of chemical physics·2025
Same author

Multivariate metal-organic frameworks enable chemical shift-encoded MRI with femtomolar sensitivity for biological systems.

Nature communications·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
查看所有相关文章

相关实验视频

Updated: May 29, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K

嵌入-搜索-调整:使用变压器模型调整DNA序列.

Pavan Holur1, K C Enevoldsen2,3, Shreyas Rajesh1

  • 1Department of Electrical and Computer Engineering, UCLA, Los Angeles, California, 90024, United States.

Bioinformatics (Oxford, England)
|February 6, 2025
PubMed
概括
此摘要是机器生成的。

我们使用无参考DNA嵌入 (RDE) 变压器开发了一种新的DNA嵌入框架 (ESA). 这种方法准确地将DNA读取与参考基因组对齐,与传统工具相匹配,并优于其他DNA-Transformer模型.

更多相关视频

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.8K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.5K

相关实验视频

Last Updated: May 29, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.3K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

15.8K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.5K

科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 机器学习 机器学习

背景情况:

  • 对基因组学而言,DNA序列对齐至关重要,传统上涉及基因组索引和读取搜索.
  • 大型语言模型 (LLM) 在编码DNA序列方面表现有前途,但分类中的表现不能保证全基因组对齐.
  • 现有的方法在有效地搜索广泛的参考基因组以获得短DNA读取时面临挑战.

研究的目的:

  • 用LLMs弥合DNA序列分类和全基因组对齐之间的差距.
  • 为准确和高效的DNA序列对齐开发一种新的框架.
  • 引入能够进行基因组规模搜索的无参考DNA嵌入模型.

主要方法:

  • 开发了"嵌入式搜索对齐" (ESA) 框架,其中包含了一个无引用DNA嵌入式 (RDE) 变压器模型.
  • 利用对比损失进行自我监督的训练,以产生丰富的,无引用的DNA序列嵌入.
  • 实现了DNA载体存储,以在参考基因组片段中进行高效,全球范围的搜索.

主要成果:

  • RDE模型在将250个长度读数与一个3千兆基基基因组的人类基因组对齐时达到99%的准确性.
  • 欧洲统计局框架的业绩竞争对手建立了诸如Bowtie和BWA-Mem.等调整工具.
  • RDE显著优于最近的DNA转换器基线 (例如,核酸转换器,海DNA),并证明了跨物种和跨染色体的可转移性.

结论:

  • 欧洲航天局框架和RDE模型为DNA序列对齐提供了一种强大的新方法.
  • 这种方法为传统的算法对齐技术提供了可行的,高精度的替代方案.
  • 无引用嵌入策略显示了推进基因组分析和大规模序列比较的潜力.