自动化:对新型蛋白质子家族的自动化基因鉴定
Adrian N Ortiz-Velez1,2, Jeet Sukumaran1,2, Ryin Rouzbehani1
1Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America.
PloS one
|January 11, 2024
概括
这项研究介绍了AutoPhy,这是一个用于遗传学聚类的自动化方法. AutoPhy有效地识别蛋白质子家族,并解决注释错误,无需手动干预或任意值.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 遗传学分析对于理解蛋白质功能,子家族和注释准确性至关重要.
- 从家族遗传树上自动化功能聚类仍然具有挑战性,因为需要手动设置值.
- 现有的方法通常依赖于任意距离,使可重复分析复杂化.
研究的目的:
- 开发一种自动化的基因组聚类方法,绕过了预定义值的需求.
- 准确地将蛋白质序列分为功能集群,并识别新型子家族.
- 解决注释错误,提高遗传学分析的可靠性.
主要方法:
- 一个新的工作流程,将统一的多重近似和投影 (UMAP) 与高斯混合模型相结合,用于自动集群.
- 实施"第二次通过"类鉴定算法,以确保单种群.
- 适用于各种蛋白质家族 (例如,外膜毛孔,乙转移酶,核受体) 和RNA病毒基因组.
主要成果:
- 通过AutoPhy方法,在精选的家族中,成功地重复了已知的蛋白质子家族.
- 自动聚类在来自Pfam,PANTHER和UniProt数据库的蛋白质家族中有效.
- 实现了对具有不同进化速率的族系的单类群的快速生成.
- 识别新型蛋白质功能组和病毒菌株,并解决错误的注释.
结论:
- 自动化提供了一个强大的,自动化解决方案,用于遗传学聚类,克服手工方法的局限性.
- 这种方法是多功能性的,适用于各种生物数据集,包括蛋白质和病毒基因组.
- 自动化增强功能关系的发现,并提高生物序列注释的准确性.
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
02:26Protein Networks
4.0K
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,...
4.0K
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
02:05Gene Evolution - Fast or Slow?
7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.1K