Jupiter-Bioinformatics-V4

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Jupiter-Bioinformatics-V4

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Jupiter Bioinformatics is a browser-based tool for interactive pairwise sequence alignment and heatmap visualization. Built on the Smith-Waterman local alignment algorithm, it renders the full scoring matrix as a color-coded heatmap on an HTML5 canvas, no installation, no server, no dependencies. Open the file and start aligning.

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Note: Although we are in 2026, an era in which AI-assisted software development has become commonplace, I would like to state explicitly that Jupiter Bioinformatics is 100% human-made. Its concept, architecture, source code, interface, testing, and documentation were created entirely through human effort, without AI-generated code or content. In other words, an actual biological human being (namely me) spent two full months designing, coding, debugging, and refining this application from scratch. And yes, I am genuinely proud of that, especially in an era when many programmers seem to have forgotten the joy of programming as both a science and an art once practiced by some of the brightest minds. Thus, use it. Abuse it. Enjoy it.

# 🧬 Jupiter Bioinformatics - V4

**Jupiter Bioinformatics** is a browser-based tool for interactive pairwise 
sequence alignment and heatmap visualization. Built on the **Smith-Waterman** 
local alignment algorithm, it renders the full scoring matrix as a color-coded 
heatmap on an HTML5 canvas - no installation, no server, no dependencies. 
Open the file and start aligning.

![Screenshot](https://github.com/Gagniuc/Jupiter-Bioinformatics-V4/blob/main/img/AI_made_image_bio_align(II).png)

## Features
- Supports **DNA, RNA, Protein, numeric, and ASCII** sequences (auto-detected)
- **11 built-in themes** for publication-ready figures
- **Drag to resize** and **scroll to zoom** the heatmap canvas
- **Fullscreen mode** for large sequence matrices
- **Copy alignment** to clipboard as Plain Text or FASTA format
- **Export PNG** - one-click heatmap download
- **LocalStorage** - save, browse, and restore up to 100 experiments
- **Zero dependencies** - single HTML file, works entirely offline

## Getting Started
1. Download or clone the repository
2. Open `index.html` in any modern browser
3. Enter two sequences and click **Run**

## References

- <i>Paul A Gagniuc, Elvira Gagniuc, [The sequence alignment problem: boundary conditions as the unifying principle](https://academic.oup.com/bib/article/27/3/bbag333/8712659), Briefings in Bioinformatics, Volume 27, Issue 3, May 2026, bbag333.</i>

***

![Screenshot](https://github.com/Gagniuc/Jupiter-Bioinformatics-V4/blob/main/img/AI_made_image_bio_align(I).png)

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