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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. 
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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
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CRISPR and crRNAs02:53

CRISPR and crRNAs

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Ribosome Profiling02:24

Ribosome Profiling

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Updated: Jun 20, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Circtools 2.0: a comprehensive framework for enhanced circular RNA bioinformatics.

Shubhada R Kulkarni1,2, Walker J Compton Mellon3, Felix Wiedmann4,5,6

  • 1Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany.

BMC Bioinformatics
|June 19, 2026
PubMed
Summary
This summary is machine-generated.

Circtools 2.0 enhances circular RNA (circRNA) research with an ensemble detection strategy, spatial profiling, cross-species analysis, and full-length characterization. This updated software offers a comprehensive toolkit for deeper mechanistic studies of circRNAs.

Keywords:
CircRNACircRNA analysisCircular RNAFull-length circRNASingle-cell circRNASpatial circRNA

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Last Updated: Jun 20, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
10:27

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Circular RNAs (circRNAs) are key gene regulators with cell-specific expression.
  • Detecting circRNAs from RNA-seq data is challenging due to the need for specialized tools to identify back-splice junctions (BSJ).
  • Previous development of circtools provided a foundation for circRNA detection and analysis.

Purpose of the Study:

  • To present circtools 2.0, a significant upgrade to the circtools software.
  • To enhance computational and experimental workflows for circular RNA research.
  • To provide a unified platform for multi-modal circRNA interrogation.

Main Methods:

  • Implemented an ensemble-based circRNA detection strategy for improved recall.
  • Developed automated circRNA padlock probe design for Xenium spatial transcriptomics.
  • Integrated cross-species circRNA conservation analysis.
  • Added native support for Oxford Nanopore sequencing for full-length circRNA characterization.

Main Results:

  • Achieved improved recall in circRNA detection through an ensemble strategy.
  • Enabled spatial circRNA profiling via automated probe design.
  • Facilitated cross-species comparative analysis of circRNAs.
  • Allowed detailed characterization of full-length circRNAs and their internal structures.

Conclusions:

  • Circtools 2.0 offers a next-generation platform for circRNA research.
  • The software integrates advanced detection, spatial profiling, conservation analysis, and full-length sequencing capabilities.
  • These advancements support deeper mechanistic studies and understanding of circRNA functions.