Optimal codon randomization via mathematical programming

DOI10.1016/J.JTBI.2013.05.034MaRDI QIDQ1790735zbMATH OpenOpenAlexWikidataFDO

Authors Yuval Nov, Danny Segev

Publication date 4 October 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2013.05.034

zbMATH Keywords

integer programmingprotein engineeringcodon randomizationdegenerate oligonucleotidesspiked oligonucleotides

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Integer programming (90C10) Computational methods for problems pertaining to biology (92-08)

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Cited in

(7)

• COStar: A D-star Lite-based dynamic search algorithm for codon optimization
• Calculating complexity of large randomized libraries
• On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices
• On the computational complexity of designing DNA randomizations in a combinatorial protein experiment
• Codon optimization by 0-1 linear programming
• Artificial evolution. An algorithm for an exploration of the amino acid sequences space
• Efficient Codon Optimization with Motif Engineering

Describes a project that uses

Uses Software

• PEDEL-AA
• GLUE-IT
• AMPL

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