COSMO: A dynamic programming algorithm for multicriteria codon optimization

Computational and Structural Biotechnology Journal
Akito Taneda, Kiyoshi Asai

Abstract

Codon optimization in protein-coding sequences (CDSs) is a widely used technique to promote the heterologous expression of target genes. In codon optimization, a combinatorial space of nucleotide sequences that code a given amino acid sequence and take into account user-prescribed forbidden sequence motifs is explored to optimize multiple criteria. Although evolutionary algorithms have been used to tackle such complex codon optimization problems, evolutionary codon optimization tools do not provide guarantees to find the optimal solutions for these multicriteria codon optimization problems. We have developed a novel multicriteria dynamic programming algorithm, COSMO. By using this algorithm, we can obtain all Pareto-optimal solutions for the multiple features of CDS, which include codon usage, codon context, and the number of hidden stop codons. User-prescribed forbidden sequence motifs are rigorously excluded from the Pareto-optimal solutions. To accelerate CDS design by COSMO, we introduced constraints that reduce the number of Pareto-optimal solutions to be processed in a branch-and-bound manner. We benchmarked COSMO for run-time and the number of generated solutions by adapting selected human genes to yeast codon usage freq...Continue Reading

References

May 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·G A Gutman, G W Hatfield
Sep 28, 2004·Nucleic Acids Research·Mario dos ReisLorenz Wernisch
Dec 9, 2004·DNA and Cell Biology·Hervé Seligmann, David D Pollock
Jun 28, 2008·Science·J Robert ColemanSteffen Mueller
Nov 24, 2011·Nucleic Acids Research·J Michael CherryEdith D Wong
Aug 1, 2012·Bioinformatics·Paulo GasparGabriela Moura
Apr 27, 2013·Bioinformatics·Thomas SchnattingerHans A Kestler
Oct 24, 2014·Frontiers in Bioengineering and Biotechnology·Nathan GouldDimitris Papamichail
Jul 18, 2015·Molecular Cell·Tessa E F QuaxJohn van der Oost
Mar 29, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Dimitris PapamichailGeorgios Papamichail
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Mar 16, 2017·Trends in Genetics : TIG·Christina E Brule, Elizabeth J Grayhack
Oct 12, 2017·Nature Reviews. Molecular Cell Biology·Gavin Hanson, Jeff Coller
Apr 29, 2019·Journal of Molecular Biology·Aikaterini AlexakiChava Kimchi-Sarfaty
Oct 5, 2019·Nucleic Acids Research·Miguel Angel MartínezMaria Nevot

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Software Mentioned

COSMO
filter
gc
Tandem Designer
CCTool
COSMO MOGA
MOGA
COSMO Optimization Strategy
distNearestParetoSol

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