RetroScan

RetroScan identifies and analyzes retrocopies in genomic sequences to detect, annotate, and compare retrocopy structures, substitution patterns, and expression.

Key Features:

• Integrated Bioinformatics Pipeline: Combines LAST, BEDtools, ClustalW2, HISAT2, StringTie, SAMtools, and Shiny for retrocopy scanning, annotation, and visualization.
• Enhanced Accuracy: Uses alignment programs and filter scripts to improve retrocopy identification and reduce false positives.
• Functional Analysis: Compares gene structures between parental genes and retrocopies, evaluates heterosense/synonymous substitutions, and calculates Ka/Ks ratio distributions.
• Expression Analysis: Computes FPKM values for retrocopies to assess gene expression levels.
• Visualization Outputs: Generates statistical data, retrocopy structures, Ka/Ks distributions, and FPKM heatmaps.

Scientific Applications:

• Gene Duplication Studies: Analyzes retrocopies to explore their roles in genome evolution and new gene generation.

Methodology:

Scans whole-genome sequences against protein-coding genes using integrated tools (LAST, BEDtools, ClustalW2, HISAT2, StringTie, SAMtools, and Shiny) in a single command, enabling identification, annotation, and visualization of retrocopies.