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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...
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...
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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Related Experiment Video

Updated: May 22, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.

Yuki Kato1, Kengo Sato, Kiyoshi Asai

  • 1Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. ykato@is.naist.jp

Nucleic Acids Research
|May 19, 2012
PubMed
Summary

Rtips offers fast and accurate RNA structure prediction tools. This computational suite, including IPknot and RactIP, efficiently analyzes RNA secondary structures and RNA-RNA interactions with pseudoknots and kissing hairpins.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Predicting RNA 2D complex structures is crucial for understanding RNA function.
  • Existing computational tools often face limitations in speed and accuracy for large datasets.
  • Pseudoknots and kissing hairpins represent complex structural motifs in RNA.

Purpose of the Study:

  • To develop a web-based tool set, Rtips, for rapid and accurate prediction of RNA 2D complex structures.
  • To provide efficient computational tools for analyzing RNA secondary structures with pseudoknots and RNA-RNA interactions with kissing hairpins.

Main Methods:

  • Rtips utilizes integer programming for its core computational tools.
  • IPknot is designed for predicting RNA secondary structures incorporating pseudoknots.
  • RactIP is developed for predicting RNA-RNA interactions involving kissing hairpins.

Main Results:

  • Rtips demonstrates significantly faster performance compared to existing services for large datasets.
  • The prediction accuracy of Rtips is comparable to or better than current state-of-the-art methods.
  • Both IPknot and RactIP offer efficient solutions for their respective prediction tasks.

Conclusions:

  • Rtips provides a valuable and efficient resource for RNA structure prediction.
  • The tool set enhances the capability to study complex RNA structures and interactions.
  • Rtips is freely accessible as a web server and stand-alone programs for the scientific community.