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Related Concept Videos

RNA-seq03:21

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 microarray-based...
RNA Structure01:23

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...
RNA Structure01:19

RNA Structure

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...
RNA Structure01:23

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 Structure01:25

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 has a double-helix structure. The...
Protein Folding Quality Check in the RER01:29

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...

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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A max-margin model for efficient simultaneous alignment and folding of RNA sequences.

Chuong B Do1, Chuan-Sheng Foo, Serafim Batzoglou

  • 1Computer Science Department, Stanford University, Stanford, CA 94305, USA. chuongdo@cs.stanford.edu

Bioinformatics (Oxford, England)
|July 1, 2008
PubMed
Summary

Researchers developed RAF (RNA Alignment and Folding), an efficient algorithm for simultaneous RNA alignment and folding. This method achieves high accuracy in secondary structure prediction and is significantly faster than existing approaches for high-throughput studies.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Accurate RNA structure analysis is crucial for various bioinformatics applications, including gene prediction and probe selection.
  • Existing methods for simultaneous RNA alignment and folding can be computationally intensive.
  • The development of efficient algorithms is needed for high-throughput RNA analysis.

Purpose of the Study:

  • To present RAF (RNA Alignment and Folding), an efficient algorithm for simultaneous alignment and consensus folding of unaligned RNA sequences.
  • To improve the speed and accuracy of computational RNA structure analysis.

Main Methods:

  • RAF utilizes sparse dynamic programming to achieve an effectively quadratic running time for simultaneous pairwise alignment and folding.
  • The algorithm exploits nucleotide pairing and alignment candidates identified by CONTRAfold or CONTRAlign.
  • A discriminative machine learning algorithm is used for parameter estimation, with RAF's dynamic programming as the inference engine.

Main Results:

  • RAF achieves accuracies equal to or surpassing current best methods for RNA multiple sequence secondary structure prediction in cross-validated tests.
  • RAF is nearly an order of magnitude faster than other simultaneous folding and alignment methods.
  • The algorithm's efficiency makes it suitable for high-throughput studies.

Conclusions:

  • RAF provides an accurate and significantly faster solution for simultaneous RNA alignment and folding.
  • The algorithm is well-suited for large-scale RNA structure analysis and bioinformatics applications.
  • RAF enhances the capabilities of computational RNA analysis tools.