LncRAnalyzer:使用RNA-Seq进行长时间非编码RNA发现的强大工作流程
Shinde Nikhil1, Habeeb Shaik Mohideen2, Raja Natesan Sella1
1Membrane Protein Interaction Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India.
The Plant journal : for cell and molecular biology
|October 17, 2025
概括
LncRAnalyzer是一种新的自动化管道,用于识别长非编码RNA (lncRNAs). 与现有方法相比,它提高了准确性,减少了错误,有助于植物研究.
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:
- 长非编码RNAs (lncRNAs) 是关键的RNA分子,缺乏蛋白质编码潜力.
- 鉴定lncRNAs是具有挑战性的,因为它们的丰度较低和复杂的表达模式.
- 从蛋白质编码转录区分lncRNAs需要复杂的过方法.
研究的目的:
- 开发一个自动化生物信息学管道,LncRAnalyzer,用于60种物种的准确 lncRNA识别.
- 通过将蛋白质编码或部分蛋白质编码转录的包含降至最低,提高lncRNA预测.
- 为分析 lncRNA 起源提供一个全面的工具,包括来自植物中可转移元素 (TE) 的来源.
主要方法:
- 开发了LncRAnalyzer,这是一个自动化管道,用于对60种物种进行重新训练的模型.
- 在工作流程中采用了八种不同的方法来完善 lncRNA 识别.
- 使用的RNA-Seq数据和已知的lncRNA/CDS序列进行了10倍的交叉验证.
- 与lncPipe,lncEvo,lncRNA-注释和植物lncPipe对比的LncR分析仪.
主要成果:
- 与标准模型和其他谷验证方法相比,LncRAnalyzer表现出卓越的性能.
- 该管道有效地减少了非蛋白质编码转录 (NPCTs) 的识别.
- 基准测试证实LncRAnalyzer比现有的管道更全面,更用户友好,更准确.
- 工作流程成功地确定了来自各种植物可移植元素 (TE) 的 lncRNA起源.
结论:
- LncRAnalyzer提供了一个强大而准确的解决方案,用于在各种物种中识别lncRNA.
- 该管道简化了lncRNA注释和分析的复杂过程.
- LncRAnalyzer是植物基因组学研究的一个有价值的工具,特别是用于研究TE衍生的lncRNAs.
相关概念视频
03:21RNA-seq
11.7K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.7K
02:24Ribosome Profiling
4.1K
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...
4.1K