https://github.com/kris96tian/crispr_app
The CRISPR gRNA Tool is a web application to identify potential guide RNA (gRNA) target sites within a given DNA sequence.
https://github.com/kris96tian/crispr_app
crispr-cas9 grna-sequence mysql-database
Last synced: 3 months ago
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The CRISPR gRNA Tool is a web application to identify potential guide RNA (gRNA) target sites within a given DNA sequence.
- Host: GitHub
- URL: https://github.com/kris96tian/crispr_app
- Owner: kris96tian
- Created: 2025-04-07T10:59:37.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-04-07T11:59:57.000Z (6 months ago)
- Last Synced: 2025-04-07T12:21:32.889Z (6 months ago)
- Topics: crispr-cas9, grna-sequence, mysql-database
- Language: HTML
- Homepage: https://crisprapp.pythonanywhere.com/
- Size: 21.5 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# CRISPR gRNA Tool
## Visit at: [https://crisprapp.pythonanywhere.com/](https://crisprapp.pythonanywhere.com/)
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## Overview
The CRISPR gRNA Tool is a web application developed using Python and Flask to assist researchers in identifying potential guide RNA (gRNA) target sites within a given DNA sequence. It focuses on the CRISPR-Cas9 system and detects 20-nucleotide sequences followed by the canonical NGG Protospacer Adjacent Motif (PAM) on the forward strand.
This tool provides a user-friendly interface to analyze DNA sequences and quickly locate potential gRNA binding sites, along with essential information for downstream analysis.
## Key Features
* **PAM Site Detection:** Identifies all occurrences of 20-nucleotide sequences followed by the 'NGG' PAM motif.
* **DNA Sequence Validation:** Ensures the input sequence contains only valid DNA bases (A, T, C, G).
* **Flexible Input:** Accepts DNA sequences with mixed casing and common whitespace characters (spaces, newlines).
* **GC Content Calculation:** Computes and displays the percentage of Guanine (G) and Cytosine (C) in each identified 20-mer guide sequence.
* **Example Sequences:** Includes pre-defined example sequences for easy testing and demonstration.
* **Analysis History:** Persists a history of analyzed sequences and their results using a MySQL database hosted on PythonAnywhere.
* **Session Management:** Allows users to start new analysis sessions with options to clear history.
* **Export Functionality:** Enables users to download individual analysis sessions (input sequence and results) as JSON files.
## Installation
To run this application locally, you will need Python 3.11 installed on your system.
1. **Clone the repository (if you have it on GitHub):**
```bash
git clone https://github.com/kris96tian/CRISPR_app.git
cd CRISPR_app
## Create a virtual environment:**
python -m venv venv
source venv/bin/activate
pip install Flask Flask-SQLAlchemy mysqlclient
##Usage:
python3 app.py
```
2. **Open your web browser:** Navigate to `http://127.0.0.1:5000/` (or the address provided in your terminal).
3. **Enter your DNA sequence:** Paste your DNA sequence into the text area on the homepage.
4. **Click "Find gRNA Targets":** The results will be displayed below the input area.
5. **Explore Examples:** Use the "Use" buttons next to the example sequences to quickly populate the input.
6. **View History:** Access the analysis history by clicking the "History" link in the navigation bar.
7. **Export Analysis:** From the history page, you can export individual analysis results as JSON files.
8. **New Session:** Use the "New Session" button on the homepage to start a fresh analysis. You'll be prompted if you want to clear the history.
## Database
The application now uses a **MySQL** database hosted on **PythonAnywhere** to store the history of analyses. The application connects to the database named `crisprapp$default` using the username `crisprapp`.
**Note for PythonAnywhere Deployment:** When deploying on PythonAnywhere, ensure that the `SQLALCHEMY_DATABASE_URI` in your `app.py` file is correctly configured with your MySQL connection details (username, password, host, and database name) as provided by PythonAnywhere. You also need to install the `mysqlclient` library in your PythonAnywhere virtual environment.