Primer3Plus

v1.0.8. (Changelog)

Github: https://github.com/jvrana/primer3-py-plus

Primer3Plus is a Python DNA primer design tool based off of primer3 1 2 and the Python primer3 wrapper https://pypi.org/project/primer3-py/.

design = Design()
t = "AGCGTCGTGTATGGTAGTGTATTTGCGTTGACGTTGCTGACGTCGTTGAGTCGT"
design.settings.template(t)
design.settings.product_size((len(t), len(t)))
design.settings.as_cloning_task()
design.run()

design = Design()
design.settings.template("AGCGTCGTGTATGGTAGTGTATTTGCGTTGACGTTGCTGACGTCGTTGAGTCGT")
design.settings.as_cloning_task()
design.settings.left_sequence("AGCGTCGTGTATGGTAGTG")
design.run_and_optimize(5)

For more info, take a look at the API Docs

For a list of design parameters available, take a look at the BoulderIO Parameters

For more examples, see the Usage Docs and some of the following:

• Cloning primers

• Setting primer sequences

• Handling primers with overhangs

• Handling long sequences

• Auto-relaxation of design params

Getting started

Installation

pip install primer3plus -U

Making a primer design task

The preferred way to start a design is to use the primer3plus.Design.settings() property, which provides many helper methods for setting parameters. If you’re using an interactive notebook or terminal, hitting TAB after typing design.settings will provide all of the standard design settings

design = Design()
design.settings.left_sequence('AGCGTCGTGTATGGTAGTG')
design.settings.template('AGGGGCGGAGGTGTAGTCGTCGTTAGCGTTAGTCTA')

You can also interact with the parameters more directly. To get the parameters, use the get method. From there you can set the value, print parameter information, set defaults

param = design.get('LEFT_SEQUENCE')

# print parameter information
print(param)

# print help url
print(param.help())

# set a new value
param.value = "AGGTAGTAT"

# set back to the default value
param.set_default()

You can set the value of the parameter using value or using the set <primer3plus.Design.set() method:

design.set('LEFT_SEQUENCE', 'AGGTATTAGTATATGATAT')

You can also access descriptors of the parameters. Since there are many parameters, this is useful in interactive environments:

design.SEQUENCE_ID.help()
design.SEQUENCE_ID.value = "Seq11123123"

To view all of the parameters as a dictionary, use:

print(dict(design.params))

Running design tasks

To run, simply use the run method:

design.run()

Provided is also a primer3 relaxation procedure, which will gradually relax parameters such as melting temperature and primer size until primer pairs are found:

design.run_and_optimize(5)  # run for max of 5 iterations

Table of Contents

• Usage
  • Setting design parameters
    • settings
    • setting from a single key-value pair
    • setting from a dictionary
    • getting help
  • Design cloning primers
  • Designing the right primer only
  • Handling overhangs
  • Handling long primer sequences
  • Design primers targeting interval
  • Relaxing parameters
  • Indexing with the primer3 results
• API Reference
  • Design
  • Parameter Interface
  • Design Parameters
    • BoulderIO Default Parameters
    • Extra/Special Parameters
• primer3plus change log
  • 1.0.8
  • 1.0.7
  • 1.0.6
  • 1.0.5
  • 1.0.4
  • 1.0.3
  • 1.0.2
  • 1.0.1
  • 1.0.0
  • 1.0.0b1
  • 1.0.0b0
  • 1.0.0a1
  • 1.0.0a

References

1

Untergasser A, Cutcutache I, Koressaar T, et al. Primer3–new capabilities and

interfaces. Nucleic Acids Res. 2012;40(15):e115. doi:10.1093/nar/gks596

2

http://primer3.ut.ee/primer3web_help.htm