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Related Experiment Video

Updated: Feb 20, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data.

Marie-Elisa Pinson¹, Romain Pogorelcnik¹, Franck Court¹

¹GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France.

Bioinformatics (Oxford, England)

|October 26, 2017

Summary

We developed CLIFinder, a bioinformatics tool to identify L1 Chimeric Transcripts (LCTs) using next-generation sequencing data. CLIFinder enables genome-wide discovery of these transcripts and can be adapted for other repetitive elements.

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Chromatin Isolation by RNA Purification ChIRP

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

L1 Chimeric Transcripts (LCTs) originate from LINE-1 elements and have been primarily studied using bioinformatics on dbEST data.
Understanding LCTs is crucial for deciphering complex transcriptomes.

Purpose of the Study:

To develop a novel bioinformatics tool, CLIFinder, for identifying LCTs.
To leverage next-generation sequencing (NGS) data for comprehensive transcriptome analysis.

Main Methods:

Development of CLIFinder, a bioinformatics tool specifically designed for LCT identification.
Utilizing stranded paired-end RNA-sequencing (RNA-seq) data for genome-wide analysis.
Adaptability of CLIFinder for studying transcription from other repeat types.

Main Results:

CLIFinder successfully identifies genome-wide transcribed chimera sequences indicative of LCTs.
The tool demonstrates high efficacy in analyzing NGS data for chimeric transcript discovery.
CLIFinder's flexibility allows for application beyond L1 elements.

Conclusions:

CLIFinder is an effective tool for the genome-wide identification of L1 Chimeric Transcripts.
The tool enhances the study of transcriptomes by enabling the analysis of NGS data.
CLIFinder offers a versatile platform for investigating transcription from various repetitive elements.