基因组数据整合教程,一种植物病例研究
Emile Mardoc1, Mamadou Dia Sow1, Sébastien Déjean2
1UCA-INRAE UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France.
BMC genomics
|January 17, 2024
概括
本教程概述了整合下一代测序 (NGS) 技术中的基因组数据的最佳实践. 它提供了一个六步指南,以解决分析大规模基因组数据集的复杂性,帮助生物发现.
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.
- 计算生物学 计算生物学
背景情况:
- 下一代测序 (NGS) 技术产生了大量的基因组数据集.
- 整合和分析这些大规模数据集在生物学中提出了重大的概念和分析挑战.
研究的目的:
- 为基因组数据集成的最佳实践提供一个实用,六步的教程.
- 为了解决与分析大规模基因组数据相关的复杂性.
主要方法:
- 设计一个数据矩阵.
- 为数据分析制定特定的生物问题.
- 选择适当的分析工具.
- 数据预处理和初步分析.
- 执行基因组数据整合过程.
主要成果:
- 描述了基因组数据集成最佳实践的六步教程.
- 该教程成功地使用公开可用的 (Populus L.) 的基因组数据进行了演示.
结论:
- 开发了一个新的图形输出,cimDiablo_v2,用于无监督的多块分析.
- 该工具有助于识别基因组数据变异和相互作用的关键驱动因素.
相关概念视频
Genomics
36.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.3K
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
Plant Breeding and Biotechnology
18.9K
Crop cultivation has a long history in human civilization, with records showing the cultivation of cereal plants beginning at around 8000 BC. This early plant breeding was developed primarily to provide a steady supply of food.
18.9K
Genome Annotation and Assembly
18.9K
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.
18.9K
Genome-wide Association Studies-GWAS
13.4K
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...
13.4K


