LeeShuaiyu/yxy_autoprimer

Primer Design Tool

Introduction

Primer Design Tool is a small tool for designing PCR primers. Users can input a DNA sequence and set primer design parameters. The tool will automatically generate primers that meet the specified conditions and display the results in a text box. The generated primers will also be highlighted in the input DNA sequence.

Installation

Make sure your system has Python 3 and pip installed. Then follow these steps:

Clone or download this project:
- Go to the project's GitHub page, click the "Code" button, and select "Download ZIP" to download, or clone the project using git:
```
git clone https://github.com/yourusername/yxy_autoprimer.git
```
Navigate to the project root directory:
- For macOS users: Open the Terminal application. You can open it in one of the following ways:
  - Use Spotlight Search: Press Command + Space, type "Terminal", and press Enter.
  - Open from the Applications folder: Go to "Applications" > "Utilities", then double-click "Terminal". In the terminal, use the cd command to navigate to the project directory, for example:
```
cd /path/to/yxy_autoprimer
```
- For Windows users: Open Command Prompt. You can open it in one of the following ways:
  - Use the search bar: Click the search icon on the taskbar, type "cmd" or "Command Prompt", and press Enter.
  - Open from the Start menu: Click the "Start" button, select "Windows System", then click "Command Prompt". In the Command Prompt, use the cd command to navigate to the project directory, for example:
```
cd C:\path\to\yxy_autoprimer
```
Install the required dependencies: In the command line, run the following command:
```
pip install -r requirements.txt
```
Run the script: In the command line, run the following command:
```
python maker.py
```

Usage Instructions

Run python maker.py to start the application.
Enter your DNA sequence in the "Enter Sequence" text box.
Enter or keep the default parameter values:
- PRIMER_MAX_POLY_X: Maximum allowable consecutive identical bases (default: 2).
- PRIMER_OPT_SIZE: Optimal primer length (default: 20).
Click the "Submit" button.
The tool will automatically design primers and display them in the results box. When you drag to select the generated primer content, the corresponding content in the input template will also be selected and highlighted.

Parameter Description

PRIMER_OPT_SIZE: Optimal primer length, default is 20. Typically between 18 and 25 bases; too short or too long can affect PCR efficiency.
PRIMER_PICK_INTERNAL_OLIGO: Whether to pick internal oligos, 0 means no, default is 0.
PRIMER_INTERNAL_OPT_SIZE: Optimal length of internal primers, default is 20.
PRIMER_INTERNAL_MIN_SIZE: Minimum length of internal primers, default is 18.
PRIMER_INTERNAL_MAX_SIZE: Maximum length of internal primers, default is 25.
PRIMER_INTERNAL_OPT_TM: Optimal annealing temperature of internal primers, default is 60.0°C.
PRIMER_INTERNAL_MIN_TM: Minimum annealing temperature of internal primers, default is 57.0°C.
PRIMER_INTERNAL_MAX_TM: Maximum annealing temperature of internal primers, default is 63.0°C.
PRIMER_INTERNAL_MAX_SELF_END: Maximum self-complementary end of internal primers, default is 8.
PRIMER_MIN_SIZE: Minimum primer length, default is 18.
PRIMER_MAX_SIZE: Maximum primer length, default is 25.
PRIMER_OPT_TM: Optimal annealing temperature of primers, default is 60.0°C.
PRIMER_MIN_TM: Minimum annealing temperature of primers, default is 57.0°C.
PRIMER_MAX_TM: Maximum annealing temperature of primers, default is 63.0°C.
PRIMER_MAX_POLY_X: Maximum allowable consecutive identical bases, default is 2. Long runs of identical bases can lead to secondary structure and non-specific binding.
PRIMER_SALT_MONOVALENT: Monovalent salt concentration, default is 50.0 mM.
PRIMER_DNA_CONC: DNA concentration, default is 50.0 nM.
PRIMER_PRODUCT_SIZE_RANGE: Product size range, default is [[100, 300]].

Developers

This tool was developed by yangxinyue and lsy, inspired by the Nature article Self-driving laboratories to autonomously navigate the protein fitness landscape. While this tool is far from achieving fully automated experimental design, it is a good starting point.

License

This project is licensed under the MIT License. For more details, please refer to the LICENSE file.

Note

This application is based on the primer3-py library. It aims to simplify the process and assist the Crop Science Laboratory of Kyushu University's Faculty of Agriculture in accelerating the automation of primer design.

LeeShuaiyu / yxy_autoprimer