使用序列相似性工具重新审视TriTryp的功能注释
Poorya Mirzavand Borujeni1, Reza Salavati1,2
1Institute of Parasitology, McGill University, Canada.
Heliyon
|December 6, 2024
概括
像PANNZER2这样的自动注释工具可以改善试虫的基因功能发现. 这项研究增强了功能注释,并确定了关键寄生虫生物中的潜在伪基因.
科学领域:
- 基因组学和生物信息学
- 寄生虫学的寄生虫学
- 分子生物学分子生物学
背景情况:
- 特里巴诺索马提德会引起人类和牲畜的重大疾病.
- 由于与模型生物的遗传学距离,tripanosomatids中的许多基因仍然没有注释.
- 自动功能注释工具对于有效的基因功能发现至关重要.
研究的目的:
- 评估 PANNZER2 工具在试类动物中实现自动化功能注释的有效性.
- 识别像TriTrypDB这样的数据库中现有的注释过程中的局限性.
- 开发用于识别试类虫基因组中的潜在伪基因的方法.
主要方法:
- 应用PANNZER2用于基因的基于序列相似性的功能注释 *Trypanosoma brucei*.
- 通过将PANNZER2结果与TriTrypDB的自动注释进行比较,分析了注释缺口.
- 通过调整开放的读取框架来评估序列签名覆盖范围来研究基因序列.
- 将分析扩展到 *Trypanosoma cruzi * 和 *Leishmania 大*.
主要成果:
- PANNZER2为*T. brucei*中的假设蛋白质提供了可靠的功能预测,突出了当前注释中的差距.
- 配对序列相似性对齐,即使有严格的切断,也成功地注释了许多蛋白质.
- 调整开放的读取框架显示了序列签名覆盖率的增加,这表明了潜在的伪基因.
- 分别为 *T. brucei*, *T. cruzi* 和 *L. major* 赋予了 2986, 3953 和 3798 个新的基因本体学 (GO) 术语.
- 确定了210,239个和29个具有T. brucei*,T. cruzi*和L. major*伪基因特征的基因.
结论:
- 配对序列相似性对齐是一种有价值的方法,用于改进试虫的自动功能基因注释.
- 该研究确定了大量的新功能注释和潜在的伪基因,跨越多个试类动物物种.
- 开发了一个脚本,以帮助研究人员识别潜在的伪基因,在这些生物体中推进基因组分析.
相关概念视频
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
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
Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Protein Families
15.2K
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...
15.2K
Peptide Identification Using Tandem Mass Spectrometry
6.4K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.4K
Protein 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


