Free AI-Assisted
Genome Dot Plot Viewer
Compare DNA or protein FASTA with interactive dot plots—zoomable k-mer/BLOSUM matching, PAF import, and SVG export—no account. Built-in AI agent assistant support.
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Key facts
| Fact | Value |
|---|---|
| Input modes | Pairwise FASTA, self-dotplot repeat analysis, PAF or BLAST tabular import |
| Supported formats | .fa, .fasta, .fa.gz (decompressed client-side); raw text paste or file upload |
| Matching algorithms | K-mer hash (DNA); BLOSUM62 sliding window (Protein); identity percentage binning |
| K-mer presets | 11, 15, 21, 31 |
| Sequence size limit | 5 MB per sequence uncompressed |
| Export options | Vector SVG, 2× raster PNG, raw coordinate TSV, contig mapping TSV |
| Runs in browser | Yes — 100% client-side execution; no server uploads |
| Account required | No |
What it does
Installing Java for Gepard or configuring command-line environments for desktop dot plot software creates friction when researchers need a quick visual comparison of contigs, plasmids, or alignment files. Static images produced by automated pipelines hide subtle structural inversions, duplications, and local sequence rearrangements until files are re-analyzed in desktop viewers. The Genome Dot Plot Viewer eliminates installation hurdles by computing sequence similarity matrices directly inside your web browser for pairwise FASTA comparisons, single-sequence self-repeat analysis, or pre-computed PAF and BLAST tabular alignment imports.
Upload or paste raw FASTA text or gzip-compressed files (.fa.gz up to 5 MB per sequence). DNA comparisons use sliding k-mer hash matching (presets 11, 15, 21, or 31), while protein sequences automatically switch to BLOSUM62 window scoring. Local sequence identity is color-binned into high-contrast visual tiers (>95% green, 90–95% blue, 75–90% orange, and <75% grey). Interactive canvas controls let you scroll to zoom, click and drag to pan, and hover over individual dots to inspect exact query and subject coordinates, contig identifiers, and percentage identity.
Filter background noise using the minimum identity threshold slider (50–100%). Toggle multi-FASTA contig boundary grid lines with optional automatic synteny sorting, or paste GFF3 annotation rows to overlay colored feature tracks across both axes. Export publication-ready vector SVG figures, high-resolution PNG rasters, raw coordinate TSV files, or contig mapping summaries with a single click.
Why researchers use it
- Inspect sequence similarity without installing Java or Python software
- Discover tandem repeats and inverted duplications via self-dotplots
- Visualize pre-computed minimap2 PAF or BLAST alignment outputs
- Protect proprietary sequence data with 100% client-side execution
- Export publication-ready SVG figures with identity color legends
- Overlay GFF3 gene annotations along query and subject axes
Best for
- Plasmid and bacterial contig synteny comparisons
- Identification of duplications and inverted repeats on single sequences
- Visual quality control following minimap2 or BLAST alignments
- Demonstrating comparative genomics concepts in educational settings
- Generating vector dot plot figures for manuscript submissions
- Fast interactive inspection of assemblies up to 5 MB per sequence
When to use this vs alternatives
Choose this viewer when you need an immediate, interactive dot plot for sequences under 5 MB or pre-computed PAF/BLAST files without installing desktop software. For whole-genome assemblies exceeding browser memory limits, compute alignment blocks with minimap2 offline and paste the resulting PAF file directly into the PAF/BLAST tab. Use the Sequence Property Calculator when computing molecular weight, GC content, or basic sequence metrics rather than 2D visual alignments.
What makes it different
Desktop dot plot utilities like Gepard and FlexiDot offer robust matching but require local runtime dependencies and static export workflows. Server-based platforms such as D-GENIES handle gigabase assembly alignments but introduce queue waiting times and server file uploads that are unnecessary for smaller contig pairs or existing PAF files. This viewer bridges the gap by delivering instant, interactive dot plot visualization directly in your browser with zero installation, full client-side privacy, live identity filtering, and SVG vector downloads across three dedicated input tabs (Pairwise, Self-Plot, and PAF/BLAST).
The workspace includes a built-in assistant to validate k-mer settings and interpret plot warnings; external agents can query via MCP (`pepkio_rapiddot-genome-viewer`).
How to get started
- Open the workspace and select the Pairwise, Self-Plot, or PAF / BLAST input tab.
- Paste sequence text or click Upload to select .fa or .fa.gz files (or paste PAF alignment rows).
- Configure K-mer size, Strand orientation, and optional GFF3 annotation rows.
- Click the Plot button to render the interactive similarity dot matrix.
- Use the mouse wheel to zoom, click-drag to pan, and adjust the Min identity slider to filter noise.
- Open the Export ▾ menu to download vector SVG figures or structured TSV coordinate tables.
Frequently asked questions
What sequence file formats and size limits are supported?
How does self-dotplot mode identify repeats and inversions?
How does the tool calculate local identity percentage and color bins?
Is my sequence data uploaded to a remote server?
Can I overlay gene features or multi-contig boundaries on the dot plot?
Can I use an AI agent or MCP with the Genome Dot Plot Viewer?
Client source code & registry
Last updated . Pepkio builds free lab calculators alongside bioinformatics CRO services.