Primer3Plus
Primer3Plus is a Python DNA primer design tool based off of Primer3 and the Python primer3 wrapper (https://pypi.org/project/primer3-py/).
import json
design = Design()
template = """
TCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCAC
ATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAG
GTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTAT
TTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGC
ATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGC
TCGAAGGCTTTAATTTGC
"""
template = template.replace('\n', '').replace(' ', '')
design.settings.template(template)
design.settings.as_cloning_task()
design.settings.primer_num_return(1)
results, explain = design.run()
print(json.dumps(results, indent=1))
print(json.dumps(explain, indent=1)){
"0": {
"PAIR": {
"PENALTY": 11.204301707622733,
"COMPL_ANY_TH": 0.0,
"COMPL_END_TH": 0.0,
"PRODUCT_SIZE": 248
},
"LEFT": {
"PENALTY": 9.027129166714644,
"SEQUENCE": "TCATGTAATTAGTTATGTCACGCTTAC",
"location": [
0,
27
],
"TM": 57.972870833285356,
"GC_PERCENT": 33.333333333333336,
"SELF_ANY_TH": 0.0,
"SELF_END_TH": 0.0,
"HAIRPIN_TH": 0.0,
"END_STABILITY": 2.34
},
"RIGHT": {
"PENALTY": 2.1771725409080886,
"SEQUENCE": "GCAAATTAAAGCCTTCGAGCG",
"location": [
247,
21
],
"TM": 58.82282745909191,
"GC_PERCENT": 47.61904761904762,
"SELF_ANY_TH": 0.0,
"SELF_END_TH": 0.0,
"HAIRPIN_TH": 38.006257959698985,
"END_STABILITY": 5.03
}
}
}
{
"PRIMER_LEFT_EXPLAIN": "considered 10, low tm 9, ok 1",
"PRIMER_RIGHT_EXPLAIN": "considered 10, low tm 3, high tm 4, ok 3",
"PRIMER_PAIR_EXPLAIN": "considered 1, ok 1",
"PRIMER_LEFT_NUM_RETURNED": 1,
"PRIMER_RIGHT_NUM_RETURNED": 1,
"PRIMER_INTERNAL_NUM_RETURNED": 0,
"PRIMER_PAIR_NUM_RETURNED": 1
}Installation
pip install primer3plus -U
Requirements
python >= 3.5
