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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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Ribosome Profiling02:24

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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.
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Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

Updated: Dec 9, 2025

Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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How bioinformatics resources work with G4 RNAs.

Joanna Miskiewicz1, Joanna Sarzynska2, Marta Szachniuk1

  • 1Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.

Briefings in Bioinformatics
|September 8, 2020
PubMed
Summary

Bioinformatic tools for analyzing DNA quadruplexes (G4s) are increasingly available. This study evaluates their utility for studying RNA quadruplexes, finding current resources have limitations for G4 RNA analysis.

Keywords:
PQS predictionRNAbioinformatics toolsdatabasesquadruplexesstructure analysis

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Quadruplexes (G4s) are nucleic acid structures with growing biomedical significance.
  • G4 formation is observed in various organisms, including humans, and is linked to diseases.
  • Existing bioinformatic tools primarily focus on DNA quadruplexes.

Purpose of the Study:

  • To review and assess the suitability of current bioinformatic resources for G4 RNA analysis.
  • To identify gaps and limitations in existing tools for handling RNA quadruplexes.
  • To provide insights into the application of bioinformatics for G4 RNA research.

Main Methods:

  • Comprehensive review of available bioinformatic resources for quadruplexes.
  • Categorization of resources into databases, prediction tools, and analysis/visualization tools.
  • Testing selected tools with custom RNA datasets to evaluate performance.

Main Results:

  • Identified distinct categories of bioinformatic resources for quadruplex analysis.
  • Demonstrated varying degrees of applicability of existing tools to G4 RNA.
  • Highlighted specific challenges encountered when using DNA-focused tools for RNA quadruplexes.

Conclusions:

  • Current bioinformatic tools show limited effectiveness for comprehensive G4 RNA analysis.
  • Further development of specialized tools is needed to support G4 RNA research.
  • The study provides a critical evaluation to guide future bioinformatic tool development for G4 RNAs.