dnachisel

DNA Chisel (complete documentation here) 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.

Example of use

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:

See this page for an overview of available specifications.

Infos

PIP installation:

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

More biology software

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

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

Release files for dnachisel 3.2.16

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for dnachisel 3.2.16
File	Size	Uploaded
dnachisel-3.2.16.tar.gz	116.2 kB	May 10, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for dnachisel 3.2.16
File	Interpreter	ABI	Platform	Reset
dnachisel-3.2.16-py3-none-any.whl 147.2 kB May 10, 2025	Python 3	none	any	Details

Total release size: 263.4 kB

Release files / dnachisel-3.2.16.tar.gz

Download URL	dnachisel-3.2.16.tar.gz
Size	116.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`de872bf5c92b110e0b3c78e09e7bacafa711a3a61ee707449574b5c096974497`
BLAKE2b-256 checksum How to use checksums	`ba843353ca63bdd00c340491b1b04bf5ffbb0fe522bf9989ff91b78fa4b1f648`
Upload date	May 10, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/Edinburgh-Genome-Foundry/DnaChisel
Publishing commit: github.com/Edinburgh-Genome-Foundry/DnaChisel/tree/68c09304341c3656f3dfe63eda37757d6a7b3917

Workflow

Publishing configuration: github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/68c09304341c3656f3dfe63eda37757d6a7b3917/.github/workflows/publish.yml
Publishing logs: github.com/Edinburgh-Genome-Foundry/DnaChisel/actions/runs/14944195017/attempts/1

Artifact

Subject: dnachisel-3.2.16.tar.gz
SHA-256 checksum: de872bf5c92b110e0b3c78e09e7bacafa711a3a61ee707449574b5c096974497 Verifying attestations

Release files / dnachisel-3.2.16-py3-none-any.whl

Download URL	dnachisel-3.2.16-py3-none-any.whl
Size	147.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`ec557276867b864a0cedb3b376f59d677c7b25699bbef884acad09131321e76f`
BLAKE2b-256 checksum How to use checksums	`20c01489e78e116c415dca9d6bccd5cc33abbd81810e0cbd8e02eb11e9099f60`
Upload date	May 10, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/Edinburgh-Genome-Foundry/DnaChisel
Publishing commit: github.com/Edinburgh-Genome-Foundry/DnaChisel/tree/68c09304341c3656f3dfe63eda37757d6a7b3917

Workflow

Publishing configuration: github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/68c09304341c3656f3dfe63eda37757d6a7b3917/.github/workflows/publish.yml
Publishing logs: github.com/Edinburgh-Genome-Foundry/DnaChisel/actions/runs/14944195017/attempts/1

Artifact

Subject: dnachisel-3.2.16-py3-none-any.whl
SHA-256 checksum: ec557276867b864a0cedb3b376f59d677c7b25699bbef884acad09131321e76f Verifying attestations