GOgetter:用于总结和可视化植物遗传数据的GO细节注释的管道
Emily B Sessa1, Rishi R Masalia2, Nils Arrigo3
1New York Botanical Garden Bronx New York USA.
Applications in plant sciences
|August 21, 2023
概括
GOgetter自动化了基因功能注释的总结和可视化,使用基因本体学 (GO) 细分类别. 这条管道通过提供对基因功能和生物过程的快速洞察,简化了基因组分析.
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.
- 分子生物学分子生物学
背景情况:
- 基因的功能性注释对于基因组分析至关重要.
- 基因本体学 (GO) 为描述基因功能提供了一个层次框架.
- 用GO细菌对GO注释进行总结对于鉴定基因组的特征至关重要,但通常是手动不切实际的.
研究的目的:
- 开发一个自动化管道来获取,总结和可视化GO细分类别.
- 为了促进数据集内的整体基因功能的表征.
主要方法:
- 在GOgetter管道中使用bash和Python脚本.
- 它处理了核酸基因序列的输入FASTA文件.
- 输出包括基因对基因基因模型命中,相关的GO术语,以及GO精细摘要/可视化.
主要成果:
- 管道确定了每个输入基因的最佳命中.
- 它检索所有与这些匹配相关的GO术语和注释.
- 为整个数据集生成总结和可视化的GO细分类别.
结论:
- GO注释作为基因功能描述的通用语言.
- GOgetter提供了一种快速和用户友好的方法来进行GO精细分析.
- 该管道有助于统计分析和下游查询基因功能数据.
相关概念视频
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
Export of Mitochondrial and Chloroplast Genes
3.7K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
3.7K
Gene Families
2.6K
2.6K
Light Acquisition
8.5K
In order to produce glucose, plants need to capture sufficient light energy. Many modern plants have evolved leaves specialized for light acquisition. Leaves can be only millimeters in width or tens of meters wide, depending on the environment. Due to competition for sunlight, evolution has driven the evolution of increasingly larger leaves and taller plants, to avoid shading by their neighbors with contaminant elaboration of root architecture and mechanisms to transport water and nutrients.
8.5K
Gene Evolution - Fast or Slow?
2.9K
2.9K
Genome Size and the Evolution of New Genes
2.5K
2.5K


