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相关概念视频

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.7K
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.
18.7K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.5K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.5K
RNA-seq03:21

RNA-seq

9.7K
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...
9.7K
DNA-only Transposons02:57

DNA-only Transposons

14.2K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.2K
lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

2.7K
2.7K
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

9.7K
Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
9.7K

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相关实验视频

Updated: May 7, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

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Cov-trans:一种高效的算法用于冠状病毒中不连续的转录组装.

Xiaoyu Guo1, Zhenming Wu1, Shu Zhang1

  • 1School of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, Shandong Province, 266071, China.

BMC genomics
|December 30, 2024
PubMed
概括

Cov-trans精确地组装了冠状病毒转录,克服了现有方法的局限性. 这种新的工具增强了病毒转录边界识别,以改善病毒学研究和抗病毒开发.

关键词:
冠状病毒 冠状病毒不连续的转录.混合整数线性编程 混合整数线性编程基于引用的组件组合

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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

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相关实验视频

Last Updated: May 7, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

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科学领域:

  • 病毒学 病毒学
  • 计算生物学 计算生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 冠状病毒利用不连续的转录来有效地复制和宿主细胞传播.
  • 准确的病毒转录组装对于病毒学研究和开发抗病毒策略至关重要.
  • 现有的转录组装算法,设计用于真核生物,不适合冠状病毒,导致转录边界确定精度低.

研究的目的:

  • 开发专门针对冠状病毒的高精度病毒转录组装算法.
  • 为了解决确定病毒转录边界的当前方法的局限性.

主要方法:

  • 提出Cov-trans,一种基于参考的转录组装器,用于冠状病毒不连续转录.
  • 使用不连续的转录机制,启动/停止编码子和读取对齐来识别正规的转录.
  • 使用混合整数线性编程,将非正规的转录组合 (non-canonical transcript assembly) 作为路径提取问题.

主要成果:

  • 与其他装配器相比,Cov-trans表现出卓越的准确性和回忆力.
  • 冠状病毒转录在准确识别病毒转录边界方面表现出色.
  • 开发的算法有效地恢复非正规的病毒转录.

结论:

  • 在组装冠状病毒转录中,Cov-trans提供了显著的进步.
  • 该工具在边界识别中的高精度是其关键优势.
  • 可用于病毒学研究和抗病毒开发的Cov-trans.