zol & fai:对基因集群进行大规模有针对性的检测和进化研究
Rauf Salamzade1,2, Patricia Q Tran3,4, Cody Martin2,3
1Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
bioRxiv : the preprint server for biology
|June 19, 2023
概括
我们开发了fai和zol用于基因集群和移动遗传元素 (MGE) 的大规模比较分析. 这些工具克服了骨科推断中的瓶,使得数千个基因组的综合分析成为可能.
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.
- 进化生物学 进化生物学
背景情况:
- 基因经常被组织成集群,包括重要的生物合成基因集群 (BGC) 和移动遗传元素 (MGE) 等.
- 在多样化的基因组中大规模分析这些集群在计算上具有挑战性,这是由于ortology推断的限制.
研究的目的:
- 引入FAI和ZOL,这两种新的计算工具旨在进行基因集群和MGEs的大规模比较分析.
- 克服现有的瓶在整形学推断全面的基因组分析在广泛的分类学上下文.
主要方法:
- fai工具可以在目标基因组数据库中识别查询基因集群的正统实例.
- zol工具对已识别的集群实例中的单个基因进行特定上下文的正义组推理.
- zol还为ortolog组提供功能注释和进化统计数据.
主要成果:
- fai和zol能够在数千个基因组中进行可扩展,可靠的基因集群和MGE的正统推断.
- 已证明的应用包括在元基因组中进行病毒追踪,发现*Aspergillus flavus* BGCs中的遗传洞察力,并分析细菌毒性基因集群进化.
结论:
- 和显著提高了基因集群和MGE大规模比较基因组学的能力.
- 这些工具为分析复杂的基因组结构及其进化动态提供了强大的解决方案.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.9K
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...
5.9K
Modern Molecular Taxonomy
56
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
56
Gene Evolution - Fast or Slow?
7.2K
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...
7.2K
DNA Microarrays
17.6K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
17.6K


