斯托尔夫-记者:发现基因之间的基因.
Nicholas J Dimonaco1,2,3,4,5, Amanda Clare2, Kim Kenobi6
1Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, Wales, UK.
Nucleic acids research
|October 28, 2023
概括
StORF-Reporter在未注释的基因组区域中识别了缺失的 prokaryotic 基因. 这个工具发现了Stop-ORFs (StORFs),恢复了通常被标准注释方法遗漏的基因,提高了基因组注释的准确性.
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:
- Prokaryotic 基因组由于注释工具的限制,包含了大量未注释的区域.
- 替代起始编码子经常导致错误报告或遗漏基因在当前注释.
研究的目的:
- 介绍StORF-Reporter,一种用于识别未注释的 prokaryotic 基因组区域中缺失的蛋白质编码基因 (CDS) 的新工具.
- 为了提高 prokaryotic 基因组注释的完整性和准确性.
主要方法:
- 从注释的基因组中提取未注释的基因组区域.
- 在这些未注释的地区内识别停止ORF (StORF).
- StORFs是开放的读取框架,由停止编码子划分,旨在捕获经常错过的基因.
主要成果:
- 斯托尔夫-记者成功地恢复了从正规基因组注释中缺席的基因.
- 对模型生物,大肠杆菌泛基因组和大型数据集 (5109个基因组) 的应用揭示了扩展的基因集合.
- 确定了新的基因家族,并将现有的家族扩展到其他属.
结论:
- 该StORF-Reporter方法有效地识别和恢复潜在的功能基因错过了标准注释管道.
- 跨属的高序列保护表明,许多已识别的StORFs代表了真正的功能基因.
- 这些发现支持将已识别的StORF纳入未来的正规基因组注释.
相关概念视频
Reporter Genes
11.4K
Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
11.4K
Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K


