DNA Chisel is a Python library to optimize the nucleotides of DNA sequences with respect to a set of constraints and optimization objectives. It can be used for codon-optimizing the genes of a sequence for a particular organism, modifying a sequence to meet the constraints of a DNA provider while preserving genes, and much more.
DNA Chisel comes with more than 15 types of optimizations and constraints and allows users to define new specifications in Python, making the library suitable for a large range of automated sequence design applications, or complex custom design projects.
Example of use
from dnachisel import *
# DEFINE THE OPTIMIZATION PROBLEM
random_sequence = random_dna_sequence(10000)
problem = DnaOptimizationProblem(
sequence=random_sequence,
constraints=[AvoidPattern(enzyme_="BsaI"),
EnforceGCContent(mini=0.3, maxi=0.7, window=50)],
objectives=[CodonOptimize(species='e_coli', location=(500, 1300))]
)
# 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())Infos
PIP installation:
pip install dnachiselWeb 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
DNA Chisel is part of the EGF Codons synthetic biology software suite for DNA design, manufacturing and validation.
1 maintainer
Metadata
1 maintainer
Release files for dnachisel 0.1.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| dnachisel-0.1.6.tar.gz | 1.0 MB | Details |
Release files / dnachisel-0.1.6.tar.gz
| Download URL | dnachisel-0.1.6.tar.gz |
|---|---|
| Size | 1.0 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
545fa808b2ac8124b1685ef00fd709b6cf9ffdd6a55f1bcdae376e3072d741aa
|
|
BLAKE2b-256 checksum How to use checksums |
3158e3c107bbfceb08be5b2e7d67c24a4cb779e59300e0591a795ddc53e8eeab
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
Python-urllib/3.6
|
