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相关概念视频

RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
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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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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Ribosome Profiling02:24

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...
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相关实验视频

Updated: Jun 29, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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RNAhugs网络服务器用于定制的3DRNA结构对齐.

Michal Zurkowski1, Mateusz Swiercz1, Filip Wozny1

  • 1Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.

Nucleic acids research
|April 8, 2024
PubMed
概括
此摘要是机器生成的。

RNAhugs是一个新的网络服务器,用于对准3DRNA结构. 它有效地找到结构之间最长的匹配碎片,并以用户定义的准确度帮助结构分析.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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科学领域:

  • 结构生物信息学 结构生物信息学
  • 计算生物学是一种计算生物学.
  • 分析RNA结构分析RNA结构分析

背景情况:

  • 3D分子结构对齐对于评估结构相似性至关重要.
  • 现有的对齐算法是计算密集型的,特别是对于大型数据集.
  • 分析RNA的3D结构需要专门的和高效的对齐工具.

研究的目的:

  • 介绍RNAhugs,一个用于灵活3DRNA结构对齐的新型Web服务器.
  • 为分析RNA中的结构相似性和子结构提供一个用户友好的平台.
  • 开发一种有效的工具,克服传统对齐方法的计算局限性.

主要方法:

  • RNAhugs使用两个高效的启发式,GEOS和GENS,用于结构对齐.
  • 服务器可以接受PDB或PDBx/mmCIF格式的RNA结构.
  • 它根据用户指定的根-平均-平方偏差 (RMSD) 切线对齐3DRNA结构.

主要成果:

  • RNAhugs识别了3DRNA结构之间最长的对应碎片.
  • 服务器可以处理多模型文件,并在单个任务中执行多个对齐 (1-25).
  • 它可以灵活地与用户定义的准确性参数对齐.

结论:

  • RNAhugs为3DRNA结构对齐提供了一种高效和灵活的解决方案.
  • 网络服务器简化了RNA分子中的结构相似性和子结构的分析.
  • RNAhugs是公开的,为科学界提供了一个可访问的工具.