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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Deep Computational Circular RNA Analytics from RNA-seq Data.

Tobias Jakobi1,2, Christoph Dieterich3,4

  • 1Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany. tobias.jakobi@med.uni-heidelberg.de.

Methods in Molecular Biology (Clifton, N.J.)
|January 12, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a bioinformatics toolbox for analyzing circular RNAs (circRNAs). The tool aids in discovering, quantifying, and reconstructing circRNA structures from sequencing data.

Keywords:
BioinformaticsCircularCircular RNA detectionRNA analysisWhole-transcriptome sequencing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Circular RNAs (circRNAs), initially termed "scrambled exons," were discovered in the 1990s.
  • High-throughput sequencing has revealed circRNAs are conserved, stable, and abundant across eukaryotes.
  • These molecules arise from back-splicing or exon skipping of linear RNA precursors.

Purpose of the Study:

  • To present a comprehensive bioinformatics toolbox for in silico circRNA analysis.
  • To cover the entire workflow from raw sequencing data to circRNA structure reconstruction.

Main Methods:

  • Utilized high-throughput whole-transcriptome sequencing data.
  • Developed and applied a bioinformatics pipeline for circRNA analysis.
  • Included steps for back-splicing junction discovery, circRNA quantitation, and structural reconstruction.

Main Results:

  • The toolbox successfully processes raw sequencing data to identify circRNAs.
  • Enables accurate quantitation of circRNA expression levels.
  • Facilitates the reconstruction of internal circRNA structures.

Conclusions:

  • The presented bioinformatics toolbox offers a complete solution for in silico circRNA research.
  • It supports researchers in analyzing the complex world of circular RNAs.
  • Aids in understanding the function and prevalence of circRNAs in various biological contexts.