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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. 
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Updated: Sep 9, 2025

Identification of Circular RNAs using RNA Sequencing
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Identification of Circular RNAs using RNA Sequencing

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Circular RNA Identification and Characterization with CircRNAFlow: A Bioinformatics Approach.

Edward A Salinas1, Yvonne J K Edwards2,3,4

  • 1Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.

Advances in Experimental Medicine and Biology
|August 31, 2025
PubMed
Summary
This summary is machine-generated.

CircRNAFlow is a new bioinformatics pipeline for identifying and characterizing circular RNAs (circRNAs) from sequencing data. This tool aids researchers in understanding the role of circRNAs in gene regulation and disease.

Keywords:
CircRNAFlowCircular RNAMicroRNA spongeNextflowRNA-binding protein locusRNA-seqTemplate for translationWorkflow development

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Circular RNAs (circRNAs) are crucial in gene regulation and disease development.
  • circRNAs function as microRNA sponges, interact with RNA-binding proteins, and can be translated.
  • The characterization of these covalently closed ring-like structures remains limited.

Purpose of the Study:

  • To introduce CircRNAFlow, a free, open-source Nextflow pipeline for in silico circRNA identification and characterization.
  • To provide a comprehensive bioinformatics analysis of circRNAs using integrated third-party software.
  • To offer a tutorial for installation, execution, and output interpretation of CircRNAFlow.

Main Methods:

  • CircRNAFlow processes paired-end FASTQ files using next-generation sequencing (NGS).
  • The pipeline integrates tools such as FastQC, Flexbar, Bowtie2, STAR, DCC, CircTest, CRAFT, ClusterProfiler, and deepTarget.
  • Outputs include expression comparison reports and functional characterization of identified circRNAs.

Main Results:

  • CircRNAFlow generates tables and graphical images detailing identified circRNAs and their characterizations.
  • Reports enable comparison of circRNA expression to host genes and across experimental groups.
  • Functional characterization explores regulatory roles through tools like CRAFT and deepTarget.

Conclusions:

  • CircRNAFlow provides a robust and user-friendly platform for circRNA analysis.
  • The pipeline facilitates deeper understanding of circRNA functions in biological processes and disease.
  • This resource, coupled with a GitHub repository, supports researchers in circRNA bioinformatics.