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相关概念视频

Ribosome Profiling02:24

Ribosome Profiling

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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...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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相关实验视频

Updated: Jun 24, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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软件包检测无注释翻译小开放阅读框架的比较 Ribo-seqq.

Gregory Tong1, Nasun Hah2, Thomas F Martinez1,3,4

  • 1Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, United States.

Briefings in bioinformatics
|June 6, 2024
PubMed
概括

识别翻译的微蛋白需要对核糖体分析 (Ribo-seq) 数据进行仔细分析. 使用多个计算工具提高了检测小开放读取 (smORF) 的信心,并考虑了数据质量变化.

关键词:
里博-seqq 的意思这是一种微型蛋白质.在 smORF 标注中使用 smORF 标注.翻译翻译翻译翻译翻译翻译

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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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科学领域:

  • 基因组学就是基因组学.
  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 对微蛋白编码小开放阅读框架 (smORF) 的准确注释对于理解细胞功能和疾病至关重要.
  • 核糖体剖析 (Ribo-seq) 是实证识别翻译smORF的主要方法,但数据集质量和分析工具差异很大.

研究的目的:

  • 评估Ribo-seq数据质量和分析工具选择对翻译smORFs识别的影响.
  • 为了比较五种常用的Ribo-seq分析工具用于smORF检测的性能.

主要方法:

  • 在高分辨率的Ribo-seq数据上,比较了五种Ribo-seq分析工具 (RibORFv0.1,RibORFv1.0,RiboCode,ORFquant,Ribo-TISH).
  • 基于smORF识别协议的工具性能评估.
  • 对Ribo-seq数据分辨率和质量的工具灵敏度的评估.

主要成果:

  • 在五种用于smORF识别的工具中观察到的一致性很低,所有工具只检测到约2%的smORF.
  • 与smORFs相比,对更大的注释基因的同意率明显高 (~74%) .
  • 一些工具对低分辨率的Ribo-seq数据显示偏差,而另一些则更强大.
  • 通过多种工具识别的smORF表现出更高的翻译水平和框架内读取分数.

结论:

  • 建议使用多个计算工具来确定微蛋白编码smORF.
  • 工具的选择应考虑Ribo-seq数据集的质量和下游smORF表征的具体目标.
  • 分析或共识方法的标准化可能是可靠的smORF发现的必要条件.