相关实验视频

Updated: Jul 16, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

AliNA - 一个深度学习程序用于RNA二级结构预测

Shamsudin S Nasaev¹, Artem R Mukanov², Ivan I Kuznetsov³

¹Institute of Biomedical Chemistry, 10, Pogodinskaya str., 119121, Moscow, Russia.

Molecular informatics

|September 14, 2023

概括

这项研究介绍了AliNA,这是一种用于预测RNA二次结构的深度学习方法. 通过使用数据增强,AliNA可以准确地预测各种RNA类型的结构,甚至包括那些不在训练数据中的结构.

科学领域:

分子生物学分子生物学
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:

许多自然和人造RNA变体在细胞过程中起着至关重要的作用.
准确预测RNA二次结构对于理解它们的功能和相互作用至关重要.
现有的预测方法,包括热力学和深度学习方法,在准确性和适用性方面存在局限性.

研究的目的:

开发一种基于深度学习的新方法,用于准确的RNA二次结构预测.
解决当前方法的局限性,特别是对于非同源RNA家族.
为RNA结构预测研究提供一个免费可访问的工具.

主要方法:

开发了AliNA (ALIgned Nucleic Acids),这是一种用于RNA二次结构预测的深度学习模型.
采用数据增强技术,利用模拟数据来扩展现有数据集.
通过各种基准验证了该方法,包括具有伪结的RNA结构.

主要成果:

阿里纳证明了高质量的RNA二次结构预测能力.
该方法成功地预测了RNA家族的结构,这些RNA家族与训练数据不一致.
在各种基准标准中表现强,包括具有伪结的复杂结构.

结论:

在RNA二次结构预测准确性和适用性方面,AliNA提供了显著的进步.
数据增强是一种有效的策略,可以改善对代表性不足的数据的深度学习模型性能.
AliNA工具在GitHub上公开提供,以促进更广泛的研究使用.

关键词:

这是一个RNARNARNARNARNA.数据增强数据增强深度学习是一种深度学习.伪结伪结伪结二级结构是二级结构的二次结构.结构预测结构预测

更多相关视频

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

相关概念视频

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

Nucleic Acid Structure

Nucleic Acid Structure

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...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

RNA-seq

RNA-seq

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...

Experimental RNAi

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...