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iPhylo套件:用于构建和注释生物和化学分类树的交互平台
Yueer Li1, Chen Peng1, Fei Chi2
1MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang 310030, China.
Briefings in bioinformatics
|December 31, 2024
概括
iPhylo套件提供了一个统一的,自动化的平台,用于构建生物和化学分类树. 该工具有助于探索生物和代谢物,增强环境和人类微生物组研究.
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
- 化学信息学 化学信息学
背景情况:
- 准确的分类学分类对于研究各种环境中的生物和代谢物至关重要.
- 对生物分类树的现有工具有局限性,对化学分类树缺乏简化方法.
研究的目的:
- 引入iPhylo套件,这是一个全面的平台,用于自动化和交互式的生物和化学分类分析.
- 为生物和化学数据构建和注释分类树提供统一的框架.
主要方法:
- 开发一个基于Web的平台和一个独立的命令行接口 (CLI).
- 整合国家生物技术信息中心 (NCBI) 分类学,ChemOnt和NPClassifier进行分类.
- 实现基于R的可视化模块,用于交互式树构建和定制.
主要成果:
- 该iPhylo套件允许交互式构建和对分类树进行注释.
- 它支持生物 (NCBI) 和化学 (ChemOnt,NPClassifier) 分类.
- 该平台有助于可视化环境微生物群和分析微生物代谢物合成.
结论:
- iPhylo套件为深入的分类学和整合性分析提供了一个统一和交互的框架.
- 它解决了对简化化学分类树结构的需求.
- 该工具增强了在各种情况下发现微生物组和代谢组之间的相关性.
相关概念视频
01:23Phylogeny
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
03:21Phylogenetic Trees
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.
02:54Evolutionary Relationships through Genome Comparisons
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...
03:21Phylogenetic Trees
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.
01:20Applications 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...
01:28Microbial Phylogeny
Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...