Efficient codon optimization with motif engineering

DOI10.1016/J.JDA.2012.04.017MaRDI QIDQ1932358zbMATH OpenOpenAlexFDO

Authors Anne Condon, Chris Thachuk

Publication date 18 January 2013

Published in Journal of Discrete Algorithms (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jda.2012.04.017

zbMATH Keywords

codon optimizationdynamic programmingmotif engineeringsequence design

Mathematics Subject Classification ID

Combinatorics on words (68R15) Computing methodologies for text processing; mathematical typography (68U15) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

Recommendations

• Efficient Codon Optimization with Motif Engineering
• Codon optimization by 0-1 linear programming
• COStar: A D-star Lite-based dynamic search algorithm for codon optimization
• Optimizing the codon usage of synthetic gene with QPSO algorithm
• Optimizing restriction site placement for synthetic genomes

Cites work

• Algorithms on Strings, Trees and Sequences
• Efficient Codon Optimization with Motif Engineering
• scientific article; zbMATH DE number 1142294 (Why is no real title available?)

Cited in

(13)

• Optimal codon randomization via mathematical programming
• Optimizing the codon usage of synthetic gene with QPSO algorithm
• Codon optimization by 0-1 linear programming
• Intragenic codon bias in a set of mouse and human genes
• A theoretical analysis of codon adaptation index of the \textit{Boophilus microplus bm86} gene directed to the optimization of a DNA vaccine
• Optimality of codon usage in \textit{Escherichia coli} due to load minimization
• 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
• The positive selection estimated by a codon substitution model with codon usage bias
• Combinatorial Pattern Matching
• Visualizing codon usage within and across genomes: concepts and tools

Describes a project that uses

Uses Software

• Codon
• UpGene
• JCat
• GeMS
• OPTIMIZER
• Gene Designer
• Synthetic Gene Designer

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