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Optimize DNA sequences under constraints.

Project description

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 dnachisel

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

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.

Project details


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