Codon optimization by 0-1 linear programming

DOI10.1016/J.COR.2020.104932MaRDI QIDQ2177826zbMATH OpenOpenAlexFDO

Authors Claudio Arbib, Alessandra Tessitore, Mustafa Ç. Pınar, Fabrizio Rossi

Publication date 6 May 2020

Published in Computers \& Operations Research (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.cor.2020.104932

zbMATH Keywords

codon optimizationinteger linear programmingmotif engineeringprotein design

Mathematics Subject Classification ID

Boolean programming (90C09) Integer programming (90C10) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

Recommendations

• Efficient codon optimization with motif engineering
• Efficient Codon Optimization with Motif Engineering
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• Optimizing the codon usage of synthetic gene with QPSO algorithm
• COStar: A D-star Lite-based dynamic search algorithm for codon optimization

Cites work

• Efficient codon optimization with motif engineering
• Finding paths in graphs avoiding forbidden transitions
• Finding paths in grids with forbidden transitions
• Optimizing Restriction Site Placement for Synthetic Genomes

Cited in

(10)

• Optimal codon randomization via mathematical programming
• Optimizing the codon usage of synthetic gene with QPSO algorithm
• Efficient codon optimization with motif engineering
• An optimization approach to gene stacking
• Two proteins for the price of one: the design of maximally compressed coding sequences
• COStar: A D-star Lite-based dynamic search algorithm for codon optimization
• Efficient Codon Optimization with Motif Engineering
• Optimizing restriction site placement for synthetic genomes
• Combinatorial Pattern Matching
• Gene mutation estimations via mutual information and Ewens sampling based CNN & machine learning algorithms

Describes a project that uses

Uses Software

• Codon
• UpGene
• GASCO

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