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--- |
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title: Protein Similarity API |
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emoji: 🧬 |
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colorFrom: blue |
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colorTo: indigo |
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sdk: docker |
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app_port: 7860 |
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python_version: 3.10 |
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short_description: FastAPI for comparing protein sequences. |
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tags: |
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- bioinformatics |
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- protein |
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- api |
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- fastapi |
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- transformer |
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- huggingface |
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pinned: true |
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--- |
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# protein-similarity-api |
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A lightweight, production-ready FastAPI service for comparing protein sequences using state-of-the-art transformer embeddings (ESM-2). |
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It provides a simple REST API to measure semantic similarity between protein sequences, returning a similarity score based on cosine distance in embedding space. |
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--- |
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## Why this matters? |
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Protein similarity is at the heart of functional annotation, homology detection, and structure prediction. This API lets anyone (researcher, student, dev) compare protein sequences using powerful models. |
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--- |
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## Features |
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- Compare two protein sequences using [ESM-2](https://huggingface.co/facebook/esm2_t33_650M_UR50D) |
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- Returns cosine similarity + classification (homologous vs. non-homologous) |
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- Lightweight, deployable on free-tier platforms like Render or Railway |
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- Clean FastAPI structure, easy to extend (e.g. embeddings endpoint, caching) |
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--- |
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## API Endpoints |
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### `POST /compare` |
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Compare two sequences and get similarity: |
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#### Request: |
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```json |
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{ |
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"sequence_1": "MSSKVIFF...", |
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"sequence_2": "MTTRLIFF...", |
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"model": "esm_2_650m" |
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} |
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``` |
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#### Response: |
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```json |
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{ |
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"cosine_similarity": 0.57, |
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"classification": "moderate similarity (possible remote homolog)", |
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"model": "ESM-2 650M" |
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} |
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``` |
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## How to run it? |
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```shell |
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python3 -m venv venv |
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source venv/bin/activate |
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pip install -r requirements.txt |
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uvicorn main:app --reload |
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``` |
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## How to deploy it? |
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``` |
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``` |
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