AutoPMD

Project Introduction

AutoPMD is automated point mutation primer design tool for high-throughput protein modification.

The main application scenarios of this software tool include:

1. Single point mutation primer design

• Description：Support the design of primers for implementing single amino acid point mutations.

2. Double point mutation primer design

• Description：Support the design of primers for implementing mutations at two amino acid sites.
  • The distance between amino acid sites of two mutations is less than or equal to 15bp
  • The distance between amino acid sites of two mutations is greater than 15bp but less than or equal to 120bp
  • The distance between amino acid sites of two mutations is greater than 120bp

Installation

python packages

We suggest using Python 3.8 for AutoPMD.

pip install -r requirements.txt

Usage & Example

Input:

• Step 1: Upload the plasmid template(gb) file and the target information(CSV) file to be edited.
• Step 2: provide the necessary configuration information.
  • Example configuration (params.json):

    {
    "pcr_single_primer_params":{
        "PRIMER_OPT_SIZE": 29,
        "PRIMER_MIN_SIZE": 27,
        "PRIMER_MAX_SIZE": 36,
        "PRIMER_OPT_TM": 65.0,
        "PRIMER_MIN_TM": 60.0,
        "PRIMER_MAX_TM": 75.0,
        "PRIMER_MIN_GC": 20.0,
        "PRIMER_MAX_GC": 80.0
        },
    "pcr_double_primer_params":{
        "PRIMER_OPT_SIZE": 29,  
        "PRIMER_MIN_SIZE": 27,
        "PRIMER_MAX_SIZE": 36,
        "PRIMER_OPT_TM": 65.0,
        "PRIMER_MIN_TM": 60.0,
        "PRIMER_MAX_TM": 75.0,
        "PRIMER_MIN_GC": 20.0,
        "PRIMER_MAX_GC": 80.0
    },
    "seq_primer_params":{
        "PRIMER_OPT_SIZE": 20,
        "PRIMER_MIN_SIZE": 18,
        "PRIMER_MAX_SIZE": 25,
        "PRIMER_OPT_TM": 65.0,
        "PRIMER_MIN_TM": 55.0,
        "PRIMER_MAX_TM": 75.0,
        "PRIMER_MIN_GC": 20,
        "PRIMER_MAX_GC": 80  
      },
    "global_params":{
        "AMPLICONIC_MARKER_SEQ_START_LENGTH": [200,100],
        "AMPLICONIC_GENE_TARGET_SEQ_LENGTH": 40    
    },   
    "input_mute_name":"自动化构建的样品引物设计.xlsx",  
    "inputdir":"/input_mut/",
    "outputdir":"/output/",
    "targetGene_after_before_seq_n":80
    }

Execute:

python main.py  -i params.json

Output:

• sucess_site_mute.zip
• failture_site_mute.zip

These files will be generated in the XXX/AutoPMD/src/data/output directory.