CLIFinder

CLIFinder identifies potential L1 Chimeric Transcripts from stranded paired-end RNA-seq data by analyzing paired-end reads in the human genome.

Key Features:

• L1 Chimeric Transcript Detection: Identifies genome-wide transcribed chimera sequences corresponding to potential LCTs initiated by repeated LINE-1 element antisense promoters that include the L1 5'UTR sequence in antisense orientation followed by the adjacent genomic region.
• Repeat Element Customization: Can be adapted to detect transcripts initiated by different repeat elements and to study transcription from other repeat types.

Scientific Applications:

• LINE-1 Transcriptome Analysis: Enables genome-wide identification of L1 Chimeric Transcripts using NGS data rather than EST-based approaches.
• Repeat Element Transcription Studies: Supports investigation of transcription from various repeat types beyond LINE-1 elements.

Methodology:

CLIFinder analyzes stranded paired-end RNA-seq data to identify potential LCTs.