具有限制的RNA序列家族的生成建模 博尔兹曼机器
Jorge Fernandez-de-Cossio-Diaz1
1Laboratory of Physics of the Ecole Normale Supérieure, CNRS UMR 8023 & PSL Research, Paris, France. jfdecd@icloud.com.
Methods in molecular biology (Clifton, N.J.)
|September 23, 2024
概括
限制波兹曼机器 (RBMs) 可以模拟复杂的RNA结构,并帮助设计基RNA,如核糖突变器. 这种机器学习方法已被验证用于生成RNA序列,为生物序列建模提供了实用的工具.
科学领域:
- 计算生物学 计算生物学
- 机器学习 机器学习
- 生物信息学是一种生物信息学.
背景情况:
- 结构性RNA分子,包括 рибо开关,具有由二级和三级结构影响的复杂序列依赖性.
- 了解和建模这些依赖关系对于预测RNA功能和设计新的RNA分子至关重要.
- 限制波兹曼机器 (RBMs) 为捕获这些复杂的序列模式提供了一个潜在的框架.
研究的目的:
- 探索受限博尔兹曼机器 (RBMs) 的应用,用于建模结构化RNA序列家族.
- 证明RBM在捕获与RNA结构和灵活性相关的序列依赖性的实用性.
- 为在生物序列建模中实施RBM提供实用指导和代码示例.
主要方法:
- 对受限制的博尔兹曼机器 (RBM) 的数学和实践介绍.
- 开发用于数据采集,RBM培训和序列采样的独立代码示例.
- 在生物序列建模中应用RBM算法的详细实现.
主要成果:
- RBM有效地模拟结构化RNA中的复杂序列依赖.
- 可以成功地将RBM应用于所有菌性RNA的设计,以 рибо开关为例.
- 实验验证证证实了RBM作为特定RNA序列家族 (例如SAM-I рибо交换机阿马域) 的生成模型.
结论:
- 限制波兹曼机器是模拟具有复杂结构特征的RNA序列家族的强大工具.
- RBMs促进了功能性RNA分子的设计,包括治疗相关的核糖突变器.
- 提供的计算工具使研究人员能够应用RBM来进行先进的生物序列建模和RNA设计.
相关概念视频
RNA Structure
4.7K
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...
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...
4.7K
Bacterial RNA Polymerase
29.4K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.4K
Ribozymes
11.2K
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can...
Ribozymes can...
11.2K
RNA-seq
9.9K
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...
9.9K
Bacterial Transcription
28.0K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.0K
Nucleic Acids
43.9K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
43.9K


