使用FunGeneTyper:一种可扩展的深度学习框架,对微生物蛋白质编码基因功能进行高度准确的分类和发现
Guoqing Zhang1,2,3, Hui Wang4, Zhiguo Zhang2
1College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
Briefings in bioinformatics
|July 15, 2024
概括
FunGeneTyper使用深度学习准确地分类抗生素耐药性和病毒性基因. 这一框架显著提高了各种微生物组中新基因的发现,超过了现有的生物信息学工具.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 高通量DNA测序产生了大量的微生物基因数据.
- 准确的新型蛋白质编码基因的功能分配仍然是一个重大挑战.
- 识别抗生素耐药性基因 (ARG) 和毒性因子对于公共卫生至关重要.
研究的目的:
- 开发FunGeneTyper,用于精确和细粒度的ARG和毒性因子基因分类的先进框架.
- 利用深度学习来增强微生物群体中的功能基因注释.
- 为元基因组学和生物技术研究人员提供一个多功能和易于使用的工具.
主要方法:
- 开发了FunGeneTyper,结合了两个新的深度学习模型:FunTrans和FunRep.
- 创建结构化数据库和支持资源,以进行可靠的基因分类.
- 使用经过实验确认的ARG数据集与远程同源序列进行严格测试.
主要成果:
- 在分类ARG和毒性因子方面,FunGeneTyper实现了高精度 (精度>0.99) 和F1得分 (>0.97).
- 与最先进的工具相比,在人类肠道,废水和土壤微生物群中发现新型ARG的表现卓越.
- 在ARG发现中超越了基于序列对齐和基于域的注释方法.
结论:
- FunGeneTyper为微生物基因功能分类提供了一个高度准确和高效的解决方案.
- 该框架的轻量级,保护隐私和插件性质提高了其可访问性和适用性.
- 预计FunGeneTyper的广泛采用将促进微生物组研究,生物技术和生物信息学.
相关概念视频
02:47Protein Families
15.3K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.3K
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
03:36Genome 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
02:26Protein Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
02:54Evolutionary 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