Skip to content

Latest commit

 

History

History
86 lines (73 loc) · 2.66 KB

README.md

File metadata and controls

86 lines (73 loc) · 2.66 KB
Raw

AutoPMD

Project Introduction

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

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.