Research-Stack/3-Mathematical-Models/genetics/Allelica

🚀 Allelica

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🧬 Allelica

Now, I know what you must be thinking — “Allelica? Who’s she?”

And no, Allelica is not a woman.

The name comes from allele — alternate forms of a gene.

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🧠 Very Quick Genetics (I promise)

Okay… but what is a gene?

A gene is a segment of DNA that codes for proteins. DNA is the genetic material that stores information and passes it down generations.

Now imagine this:

• A gene is like a chapter in a book (say, eye colour), everyone had the same chapter
• The slightly different versions of that chapter? → alleles

And since you inherit one copy from each parent, you always have two alleles → this pair is your genotype.

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👀 Simple Example

Let’s say:

• B → brown eyes (dominant)
• b → blue eyes (recessive)

Then:

• BB → brown
• Bb → brown (but carries blue)
• bb → blue

This is why two brown-eyed parents can still have a blue-eyed child.

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🧬 Tiny Note (before a biologist attacks me)

Yes, this is simplified. Real genetics is messier. This is just enough for this project.

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📐 The Math Side of Allelica

Allelica works on the Hardy–Weinberg principle.

p^2 + 2pq + q^2 = 1

Where:

• p = frequency of dominant allele
• q = frequency of recessive allele

And:

• p² → homozygous dominant
• 2pq → heterozygous
• q² → homozygous recessive

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📊 Example

If:

• q = 0.3 → blue allele
• p = 0.7

Then:

• q² = 0.09 → 9% blue-eyed
• p² = 0.49 → 49% BB
• 2pq = 0.42 → 42% carriers

These values stay constant unless external factors interfere.

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🤖 So… what does Allelica actually do?

She:

• Takes allele frequency data
• Calculates genotype frequencies using Hardy–Weinberg
• Compares and visualizes them across 4 populations

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🌍 Why I made this

This started with me thinking:

“Does UV or altitude affect allele frequencies?”

Then I found real examples (like malaria resistance varying by region), and that turned into:

👉 let’s build something that visualizes this

This was originally my class 12 project (very ugly version). This is the upgraded one.

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🎥 Preview

📊 Genotype Frequencies

📊 Genotype Comparison

📈 Allele Frequencies

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📊 Data Source

All allele frequency data was sourced from: gnomAD (Genome Aggregation Database)

Gene	Trait	RS Number
TYR	Skin Pigmentation	rs1042602
MC1R	Skin Pigmentation	rs1805007
SLC24A5	Skin Pigmentation	rs111310111
EPAS1	Altitude Adaptation	rs6743991
HBB	Sickle Cell Trait	rs10768683
LCT	Lactase Persistence	rs2304371
FTO	Obesity Risk	rs62033438
CFTR	Cystic Fibrosis	rs113993960
ACKR1	Malaria Resistance	rs2814778
APOE	Alzheimers Risk	rs440446

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⚙️ How to Run

Install dependencies:

pip install pandas numpy matplotlib

Run:

python Allelica.py

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✨ Features

• 📊 Genotype frequency comparison across populations
• 🔬 Genotype comparison across genes
• 📈 Allele frequency visualization
• 📋 Console summaries with biological interpretation
• ✅ Input validation
• 💾 CSV output of results

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🚀 Future Improvements

• 🗺️ v1.1 — Allele frequency heatmap across all genes and populations
• 🧬 v2.0 — BioPython integration for direct database querying instead of manual CSV input
• 🖤 v3.0 — Frontend interface (Allelica deserves to look as good as she works)

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💡 Final Note

I could keep talking about genetics forever.

But this project is basically that — just with Python and graphs.