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Related Concept Videos

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...
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...
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...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

Julien Allali1, Cédric Saule, Cédric Chauve

  • 1LaBRI, UMR 5800 CNRS, Université Bordeaux, 351, Cours de la Libération, 33405 Talence Cédex, France.

Advances in Bioinformatics
|June 8, 2012
PubMed
Summary

Comparing RNA secondary structures is vital for identifying noncoding RNAs. BRASERO is a new website providing tools to evaluate software for RNA structure comparison using diverse datasets.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pairwise comparison of RNA secondary structures is crucial for identifying noncoding RNA (ncRNA) candidates in genomic data.
  • Numerous computational tools exist for RNA structure comparison, employing varied models and algorithms.

Purpose of the Study:

  • To introduce BRASERO, a web-based platform designed for the evaluation of RNA secondary structure comparison software.
  • To provide a standardized method for assessing the performance of different RNA comparison tools.

Main Methods:

  • Development of the BRASERO website, offering a suite of evaluation tools.
  • Utilizing both real and synthetic biological datasets for comprehensive software testing.
  • Implementation of various comparison models (e.g., trees, forests, arc annotated sequences) and computational principles (e.g., edit distance, alignment).

Main Results:

  • BRASERO provides a centralized resource for benchmarking RNA structure comparison algorithms.
  • The platform facilitates the objective assessment of software performance across different datasets and methodologies.
  • Enables researchers to select the most appropriate tools for their specific RNA analysis needs.

Conclusions:

  • BRASERO serves as a valuable resource for the bioinformatics community, enhancing the reliability of RNA structure comparison.
  • The availability of standardized evaluation tools promotes the development and adoption of robust computational methods in ncRNA research.