https://github.com/edinburgh-genome-foundry/zymp

:scissors: Design compact restriction sites arrays (python utility)
https://github.com/edinburgh-genome-foundry/zymp

dna-assembly restriction-sites sequence-design synthetic-biology

Last synced: 5 months ago
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:scissors: Design compact restriction sites arrays (python utility)

• Host: GitHub
• URL: https://github.com/edinburgh-genome-foundry/zymp
• Owner: Edinburgh-Genome-Foundry
• License: mit
• Created: 2019-01-17T16:25:59.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-05-07T21:03:29.000Z (almost 3 years ago)
• Last Synced: 2024-11-17T03:10:36.782Z (5 months ago)
• Topics: dna-assembly, restriction-sites, sequence-design, synthetic-biology
• Language: Python
• Homepage: https://cuba.genomefoundry.org/design-sites-arrays
• Size: 138 KB
• Stars: 9
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

Awesome Lists containing this project

README

        
.. raw:: html

    


    

    


    


.. image:: https://github.com/Edinburgh-Genome-Foundry/zymp/actions/workflows/build.yml/badge.svg

    :target: https://github.com/Edinburgh-Genome-Foundry/zymp/actions/workflows/build.yml

    :alt: GitHub CI build status

.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/zymp/badge.svg?branch=master

   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/zymp?branch=master

**Zymp** is a Python library to produce small sequences of DNA packed with enzyme

restriction sites. You specify the enzymes you want, the ones you don't want,

whether you want the sites to be unique, or any other condition, and Zymp will

attempt to find a compact sequence verifying all of this (it really focuses on

sequence shortness).

**Warning:** Zymp is implemented with a "whatever works well enough"

philosophy. It has a lot of "whatever" but it generally works "well enough".

The algorithm is greedy with many simplifications so don't expect perfect solutions.

Examples

--------

Here is how you design a sequence

.. code:: python

    from zymp import (stacked_sites_array, plot_sequence_sites,

                  annotate_enzymes_sites, write_record)

    enzymes_names = [

        'AccI', 'AclI', 'AflII', 'AflIII', 'AgeI', 'ApaLI', 'AseI',

        'AvaI', 'BamHI', 'BanII', 'BlnI', 'BmtI', 'BsmI', 'BssHII',

        'DdeI', 'DraI', 'Eco47III', 'EcoRI', 'EcoRV', 'HindII',

        'HindIII', 'HinfI', 'HpaI', 'KpnI', 'MfeI', 'MluI',

        'MspA1I', 'MunI', 'NaeI', 'NcoI', 'NdeI', 'NheI', 'NotI',

        'NsiI', 'NspI', 'PstI', 'PvuI', 'PvuII', 'SacI', 'SacII',

        'SalI', 'ScaI', 'SfaNI', 'SnaBI', 'SpeI', 'SphI', 'SspI',

        'StyI', 'VspI', 'XhoI', 'XmaI', 'ZraI'

    ]

    forbidden_enzymes=['BsmBI', 'BsaI']

    # DESIGN AN OPTIMIZED SEQUENCE WITH ZYMP

    seq, sites_in_seq, leftover = stacked_sites_array(

            enzymes_names, forbidden_enzymes=forbidden_enzymes,

            unique_sites=True, tries=100)

    print ("Sequence length:", len(seq),

        "\nRestriction sites:", len(sites_in_seq),

        "\nSites not included: ", leftover)

                    

    # PLOT A SUMMARY

    ax = plot_sequence_sites(seq, enzymes_names)

    ax.figure.savefig("stacked_array.pdf", bbox_inches='tight')

                    

    # WRITE THE SEQUENCE AND SITE ANNOTATIONS AS A RECORD

    record = annotate_enzymes_sites(

        seq, enzymes_names, forbidden_enzymes=forbidden_enzymes)

    write_record(record, 'stacked_site_array.gb')

**Plot output:**

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**Console output:**

.. code:: bash

    Sequence length: 159

    Restriction sites: 49

    Sites not included:  {'NcoI', 'HpaI', 'SacII'}

Zymp has created a 159-nucleotide sequence with 49 of the 52 restriction sites

we specified, that's only ~3 nucleotides per site ! and the sequence is free

of BsaI or HpaI sites, so it is compatible with Golden Gate assembly.

If NcoI and HpaI are your favorite enzymes, you may be disappointed that they

are not in the final sequence. Zymp allows you to add validity conditions

for the result:

.. code:: python

    from zymp import stacked_sites_array

    def success_condition(seq, sites_in_seq, leftover):

        return {'NcoI', 'HpaI'}.issubset(sites_in_seq)

    seq, sites_in_seq, leftover = stacked_sites_array(

            enzymes_names, forbidden_enzymes=forbidden_enzymes,

            tries=100, success_condition=success_condition)

    print ("Sequence length:", len(seq),

        "\nRestriction sites:", len(sites_in_seq),

        "\nSites not included: ", leftover)

**New console output:**

.. code:: bash

    Sequence length: 158 

    Restriction sites: 47 

    Sites not included:  {'SacII', 'SacI', 'XhoI', 'BlnI', 'XmaI'}

Installation

------------

You can install zymp through PIP:

.. code::

    pip install zymp

Alternatively, you can unzip the sources in a folder and type:

.. code::

    python setup.py install

License = MIT

-------------

Zymp is an open-source software originally written at the

`Edinburgh Genome Foundry `_ by

`Zulko `_ and

`released on Github `_

under the MIT licence (Copyright 2018 Edinburgh Genome Foundry).

Everyone is welcome to contribute!

More biology software

---------------------

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png

  :target: https://edinburgh-genome-foundry.github.io/

Zymp is part of the `EGF Codons `_ synthetic biology software suite for DNA design, manufacturing and validation.