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Updated: Feb 11, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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CirComPara: A Multi-Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA-seq Data.

Enrico Gaffo1, Annagiulia Bonizzato2, Geertruy Te Kronnie3

  • 1Department of Molecular Medicine, University of Padova, Padova 35131, Italy. enrico.gaffo@gmail.com.

Non-Coding RNA
|April 17, 2018
PubMed
Summary

CirComPara is a new bioinformatics tool that detects and quantifies circular RNAs (circRNAs) from RNA sequencing data. This method enhances understanding of the circRNAome and its role in molecular pathobiology.

Keywords:
circular RNACirComParaQuakingRNA‐seqbioinformatics pipelinemonocytes

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Circular RNAs (circRNAs) are recently recognized regulatory molecules with significant roles in eukaryotes.
  • circRNAs are promising disease biomarkers due to their detectability.
  • Computational methods are crucial for identifying circRNAs from RNA sequencing (RNAseq) data.

Purpose of the Study:

  • To present CirComPara, an automated bioinformatics pipeline for circRNA detection, quantification, and annotation.
  • To integrate multiple backsplice identification methods for robust circRNA discovery.
  • To compare circRNA expression with linear RNA and gene expression levels.

Main Methods:

  • Development of CirComPara, an automated pipeline utilizing four distinct backsplice identification tools.
  • Application of CirComPara to RNAseq data from monocyte and macrophage samples.
  • Analysis of circRNA expression in relation to Quaking (QKI) haploinsufficiency.

Main Results:

  • CirComPara successfully detects, quantifies, and annotates circRNAs from RNAseq data.
  • The pipeline provides simultaneous quantification of linear RNAs and gene expression.
  • Analysis revealed biologically relevant circRNA expression patterns in response to QKI modulation.

Conclusions:

  • CirComPara offers a robust and comprehensive approach for circRNA analysis.
  • The tool facilitates deeper exploration of the circRNAome and its contribution to molecular pathobiology.
  • CirComPara aids in advancing computational and experimental studies of circRNAs.