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204 lines
4.5 KiB
Markdown
204 lines
4.5 KiB
Markdown
# 🚀 **Allelica**
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<p align="center">
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<img src="https://img.shields.io/badge/Python-3.10+-blue?style=for-the-badge&logo=python">
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<img src="https://img.shields.io/badge/Domain-Genetics-green?style=for-the-badge">
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<img src="https://img.shields.io/badge/Data-gnomAD-orange?style=for-the-badge">
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<img src="https://img.shields.io/badge/Status-Active-success?style=for-the-badge">
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</p>
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---
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## 🧬 **Allelica**
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Now, I know what you must be thinking —
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**“Allelica? Who’s she?”**
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And no, *Allelica is not a woman.*
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The name comes from **allele** — alternate forms of a gene.
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---
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## 🧠 **Very Quick Genetics (I promise)**
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Okay… but what is a gene?
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A **gene** is a segment of DNA that codes for proteins.
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DNA is the genetic material that stores information and passes it down generations.
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Now imagine this:
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* A gene is like a *chapter in a book* (say, eye colour), everyone had the same chapter
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* The *slightly different versions* of that chapter? → **alleles**
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And since you inherit one copy from each parent, you always have **two alleles** → this pair is your **genotype**.
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---
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## 👀 **Simple Example**
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Let’s say:
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* **B** → brown eyes (dominant)
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* **b** → blue eyes (recessive)
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Then:
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* **BB** → brown
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* **Bb** → brown (but carries blue)
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* **bb** → blue
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This is why two brown-eyed parents can still have a blue-eyed child.
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---
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## 🧬 **Tiny Note (before a biologist attacks me)**
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Yes, this is simplified. Real genetics is messier. This is just enough for this project.
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---
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## 📐 **The Math Side of Allelica**
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Allelica works on the **Hardy–Weinberg principle**.
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$$
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p^2 + 2pq + q^2 = 1
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$$
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Where:
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* **p** = frequency of dominant allele
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* **q** = frequency of recessive allele
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And:
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* **p²** → homozygous dominant
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* **2pq** → heterozygous
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* **q²** → homozygous recessive
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---
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### 📊 Example
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If:
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* q = 0.3 → blue allele
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* p = 0.7
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Then:
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* q² = 0.09 → **9% blue-eyed**
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* p² = 0.49 → **49% BB**
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* 2pq = 0.42 → **42% carriers**
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These values stay constant unless external factors interfere.
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---
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## 🤖 **So… what does Allelica actually do?**
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She:
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* Takes allele frequency data
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* Calculates genotype frequencies using Hardy–Weinberg
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* Compares and visualizes them across **4 populations**
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---
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## 🌍 **Why I made this**
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This started with me thinking:
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> *“Does UV or altitude affect allele frequencies?”*
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Then I found real examples (like malaria resistance varying by region),
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and that turned into:
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👉 *let’s build something that visualizes this*
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This was originally my class 12 project (very ugly version).
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This is the upgraded one.
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---
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## 🎥 **Preview**
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### 📊 Genotype Frequencies
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### 📊 Genotype Comparison
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### 📈 Allele Frequencies
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---
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## 📊 **Data Source**
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All allele frequency data was sourced from:
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[gnomAD (Genome Aggregation Database)](https://gnomad.broadinstitute.org/)
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| Gene | Trait | RS Number |
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| ------- | ------------------- | ----------- |
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| TYR | Skin Pigmentation | rs1042602 |
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| MC1R | Skin Pigmentation | rs1805007 |
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| SLC24A5 | Skin Pigmentation | rs111310111 |
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| EPAS1 | Altitude Adaptation | rs6743991 |
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| HBB | Sickle Cell Trait | rs10768683 |
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| LCT | Lactase Persistence | rs2304371 |
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| FTO | Obesity Risk | rs62033438 |
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| CFTR | Cystic Fibrosis | rs113993960 |
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| ACKR1 | Malaria Resistance | rs2814778 |
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| APOE | Alzheimers Risk | rs440446 |
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---
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## ⚙️ **How to Run**
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Install dependencies:
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```bash
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pip install pandas numpy matplotlib
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```
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Run:
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```bash
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python Allelica.py
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```
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---
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## ✨ **Features**
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* 📊 Genotype frequency comparison across populations
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* 🔬 Genotype comparison across genes
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* 📈 Allele frequency visualization
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* 📋 Console summaries with biological interpretation
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* ✅ Input validation
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* 💾 CSV output of results
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---
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## 🚀 **Future Improvements**
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- 🗺️ **v1.1** — Allele frequency heatmap across all genes and populations
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- 🧬 **v2.0** — BioPython integration for direct database querying
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instead of manual CSV input
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- 🖤 **v3.0** — Frontend interface (Allelica deserves to look as good
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as she works)
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---
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## 💡 **Final Note**
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I could keep talking about genetics forever.
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But this project is basically that —
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just with Python and graphs.
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