矩阵:用于大基因家族可扩展研究的紧和交互式可视化
Victor Rossier1,2,3, Clement Train1, Yannis Nevers1,2
1Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Genome biology and evolution
|May 14, 2024
概括
Matreex是一个新的工具,通过使用基因谱来可视化大型基因家族,以减少信息丢失. 这种动态可视化有助于进化分析,大规模的基因存在缺失研究和教育宣传.
科学领域:
- 进化生物学是进化的生物学.
- 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:
- 基因家族进化研究需要有效的可视化.
- 越来越多的基因组数据挑战了当前的基因树可视化方法.
- 现有的工具迫使人们在完整但无法管理的树木或带有隐藏信息的倒塌树木之间做出选择.
研究的目的:
- 介绍Matreex,一个用于扩展基因家族可视化的动态工具.
- 尽量减少信息损失在子树崩使用遗传学概况.
- 促进精确的进化分析和大规模的基因存在缺席研究.
主要方法:
- 开发了Matreex,一个新的动态可视化工具.
- 利用"家族遗传学"资料来表示密集的基因谱.
- 应用Matreex到MutS家族,内运输基因和视觉光.
主要成果:
- 证明了Matreex在分析大型多复制基因家族 (MutS) 的实用性.
- 在22个基因家族和622个物种中进行大型自动化基因存在缺席分析.
- 报告称,Thelohanellus kitauei. 鱼群内鞭内传输已经完全丧失.
- 展示了Matreex在为教学创造可解释数字方面的潜力.
结论:
- Matreex有效地扩展了基因家族可视化,克服了现有方法的局限性.
- 植物遗传特征是最大限度地减少信息丢失的关键.
- 马特里克斯支持从详细的进化研究到教育目的的各种应用.
相关概念视频
Gene Families
8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.8K
Genetic Screens
4.9K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
4.9K
Gene Duplication and Divergence
6.1K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.1K
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
Genome-wide Association Studies-GWAS
13.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.3K
Pedigree Analysis
84.2K
Overview
84.2K


