dnachisel

DNA Chisel

DNA Chisel (complete documentation here <https://edinburgh-genome-foundry.github.io/DnaChisel/>_) is a Python library for optimizing DNA sequences with respect to a set of constraints and optimization objectives. It comes with over 15 classes of sequence specifications which can be composed to, for instance, codon-optimize genes, meet the constraints of a commercial DNA provider, avoid homologies between sequences, tune GC content, or all of this at once!

DNA Chisel also allows users to define their own specifications in Python, making the library suitable for a large range of automated sequence design applications, and complex custom design projects. It can be used as a Python library, a command-line interface, or a web application <https://cuba.genomefoundry.org/sculpt_a_sequence>_.

Example of use

.. code:: python

from dnachisel import *

# DEFINE THE OPTIMIZATION PROBLEM

some_sequence = random_dna_sequence(10000)
problem = DnaOptimizationProblem(
    sequence=some_sequence,
    constraints=[
        AvoidPattern("BsaI_site"),
        EnforceGCContent(mini=0.3, maxi=0.7, window=50),
        EnforceTranslation(location=(500, 1400))
    ],
    objectives=[CodonOptimize(species='e_coli', location=(500, 1400))]
)

# SOLVE THE CONSTRAINTS, OPTIMIZE WITH RESPECT TO THE OBJECTIVE

problem.resolve_constraints()
problem.optimize()

# PRINT SUMMARIES TO CHECK THAT CONSTRAINTS PASS

print(problem.constraints_text_summary())
print(problem.objectives_text_summary())

Alternatively, DNA Chisel lets you define problems by annotating a Genbank file. You can also define a problem by annotating directly a Genbank as follows:

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/DnaChisel/master/docs/_static/images/example_sequence.png :alt: [logo] :align: center :width: 450px

See this page <https://edinburgh-genome-foundry.github.io/DnaChisel/ref/builtin_specifications.html>_ for an overview of available specifications.

Infos

PIP installation:

.. code:: bash

pip install dnachisel[reports]

(you can omit the [reports] suffix if you intend to use dnachisel only for sequence optimization, without generating figures or PDF reports)

Web documentation:

<https://edinburgh-genome-foundry.github.io/DnaChisel/>_

Github Page

<https://github.com/Edinburgh-Genome-Foundry/DnaChisel>_

Live demo

<http://cuba.genomefoundry.org/sculpt_a_sequence>_

License: MIT, Copyright Edinburgh Genome Foundry

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/

DNA Chisel is part of the EGF Codons <https://edinburgh-genome-foundry.github.io/>_ synthetic biology software suite for DNA design, manufacturing and validation.