Related Experiment Video
Updated: Sep 9, 2025
08:25
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
12.4K
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
Summary
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.
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.
Related Concept Videos
03:21RNA-seq
10.4K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.4K
02:24Ribosome Profiling
3.6K
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...
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...
3.6K