Polymerase-go

Polymerase-go is a high-performance, open-source computational biology workbench. Built for speed and rigorous scientific accuracy, it provides a tailored suite of tools for synthetic biology, sequence analysis, and DNA manipulation.

Whether you are a student learning the ropes of genetic engineering or a researcher needing quick, reliable sequence operations, Polymerase-go offers a streamlined, easy-to-use interface backed by the super-fast Go poly library.

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Table of Contents

• Features
  • Analysis
  • Manipulation
  • Synthetic Biology
  • Utilities
• Installation Guide
  • Prerequisites
  • Step-by-Step Setup
• Deployment on Ubuntu
• API Reference
• Contributing
• Credits

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Features

We've organized our tools into logical categories to help you find exactly what you need.

Analysis

Powerful tools to interrogate your sequences.

• Sequence Search: Locate patterns and compare sequences using advanced BWT (Burrows-Wheeler Transform) and Mash (MinHash) algorithms.
• Global & Local Align: Align sequences end-to-end (Needleman-Wunsch) or find local similarities (Smith-Waterman).
• Sequence Checks: Instantly validate GC content, check for palindromes, and confirm DNA/RNA identity.
• Alphabet Validator: Strict validation against standard (DNA, RNA, Protein) or custom user-defined alphabets.
• Folding: Predict secondary structures and Minimum Free Energy (MFE) using the Zuker algorithm.
• SeqHash: Generate collision-resistant, stable hashes for sequence deduplication.

Manipulation

Transform and edit your genetic data.

• Sequence Transform: Perform reverse, complement, and IUPAC variant expansion in one place.
• Translation: Convert DNA/RNA into protein sequences using standard genetic codes.
• Random Generator: Create synthetic test sequences of any length with balanced distribution.
• Reverse Complement: A quick utility for standard reverse complement operations.

Synthetic Biology

Design and simulate constructs.

• Golden Gate Assembly: Simulate digestion and ligation with Type IIS enzymes (BsaI, BbsI, BtgZI) for complex cloning workflows.
• Codon Optimization: Optimize protein sequences for efficient expression in host organisms like E. coli.
• Primer Design: Automatically generate forward and reverse PCR primers with calculated melting temperatures.

Utilities

Essential helpers for your workflow.

• Universal Converter: Seamlessly convert between FASTA, GenBank, FASTQ, GFF, and PolyJSON formats.

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Installation Guide

Run Polymerase-go locally on your machine for development or personal use.

Prerequisites

• Go (v1.23 or later): Download Go
• Node.js (v18 or later): Download Node.js
• Git: Download Git

Step-by-Step Setup

1. Clone the Repository

   git clone https://github.com/chiragroy2007/polymerase-go.git
   cd polymerase-go

2. Start the Backend Server The Go backend handles all computational heavy lifting.

   # Runs the server on localhost:8080
   go run main.go

   Keep this terminal open.

3. Start the Frontend Open a new terminal window to run the Next.js interface.

   npm install
   npm run dev

4. Access the Workbench Open your browser and navigate to http://localhost:3000.

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Deployment on Ubuntu

Ready to host this for your lab or team? Here is a complete guide to deploying Polymerase-go on a fresh Ubuntu server.

1. Prepare the Server

Update your system and install necessary dependencies.

sudo apt update && sudo apt upgrade -y
sudo apt install git curl build-essential -y

2. Install Go

# Download Go 1.23 (check https://go.dev/dl/ for latest version)
wget https://go.dev/dl/go1.23.0.linux-amd64.tar.gz
sudo rm -rf /usr/local/go && sudo tar -C /usr/local -xzf go1.23.0.linux-amd64.tar.gz
echo 'export PATH=$PATH:/usr/local/go/bin' >> ~/.profile
source ~/.profile
go version # Verify installation

3. Install Node.js

curl -fsSL https://deb.nodesource.com/setup_20.x | sudo -E bash -
sudo apt install -y nodejs
node -v # Verify installation

4. Deploy the Application

Clone the repo and set it up.

git clone https://github.com/chiragroy2007/polymerase-go.git
cd polymerase-go

# Build the Backend
go build -o server main.go

# Install Frontend Dependencies and Build
npm install
npm run build

5. Run the Services

For a production setup, we recommend using pm2 to keep things running.

sudo npm install -g pm2

# Start Backend
pm2 start ./server --name "poly-backend"

# Start Frontend
pm2 start npm --name "poly-frontend" -- start

Your app is now live!

• Frontend: http://<your-server-ip>:3000
• Backend: http://<your-server-ip>:8080

(Note: For a secure production environment, consider setting up Nginx as a reverse proxy with SSL.)

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API Reference

The backend exposes a RESTful API at /api. Each tool has a corresponding endpoint.

Endpoint	Method	Description
/api/align	POST	Sequence alignment (Global/Local)
/api/clone	POST	Golden Gate cloning simulation
/api/transform	POST	Sequence transformation and variants
/api/io	POST	File format conversion
...	...	See main.go for full route list

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Contributing

We welcome contributions! Whether it's fixing a bug, improving documentation, or adding a new algorithm, your help makes this tool better for everyone.

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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Credits

Polymerase-go is proudly developed by Chirag as part of TeamNeuron Tools.

• Powered by the Poly library for Go.
• Part of the TeamNeuron initiative to democratize scientific software.

_{Made with ❤️ for Biology}