Gene Exon Painter – Manual

An interactive exon painter — a web tool to visualize exon structures within transcripts and their positions on the genomic sequence.

🧬 What this tool does

• Load a genomic sequence file (.txt or .fasta) and one or more exon .fasta files.
• Display the genomic sequence with exons highlighted by color.
• Support overlapping exons using gradients.
• Auto-scroll to selected exon; tooltips on hover.
• Multiple highlights per transcript; switching transcript clears selection.
• Exons listed in dropdown, side panel, and compact table.

📂 How to use it

1. Open index.html in your browser.
2. Upload a genomic sequence file (.txt or .fasta).
3. Upload one or more exon .fasta files.
4. Select a transcript and highlight its exons.

📄 Input file formats

Genomic sequence

• Plain string; headers (>) ignored.
• Must match coordinates used in exon files.

Exons

• Header format: >ENSMUST00000000000:TranscriptName:Ex.1
• Sequences must match exact genomic regions.

✅ Browser compatibility

• Chrome
• Firefox
• Edge

This app runs entirely in the browser — no backend or server needed.

📌 Default behavior

No data is preloaded. Users must load files manually. Example files are in the exons_painter folder.