Visualizing Codon Usage Within and Across Genomes: Concepts and Tools

DOI10.1007/978-981-15-2445-5_13zbMath1460.92136OpenAlexW3004254010MaRDI QIDQ5856207

Bohdan Ostash, Maria Anisimova

Publication date: 25 March 2021

Published in: Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-981-15-2445-5_13

zbMATH Keywords

genetic codecoding sequence evolutioncodon contextcodon index

Mathematics Subject Classification ID

Genetics and epigenetics (92D10)

Uses Software

• MEGA
• PAML
• BEAST
• SimPhy
• RNAstructure
• CodonO
• JCat
• OPTIMIZER
• CodonPhyML
• HyPhy
• ACUA
• SLiM 2
• Datamonkey
• XRate
• ntCard
• KAT
• JSpeciesWS
• TETRA
• FramePlot
• DAMBE7
• INCA
• CodonW
• ExtRamp
• CAIcal
• GCUA
• stAIcalc
• FRESCo
• EasyCodeML
• MACSE
• RevTrans
• xREI
• ALF
• CodonTest
• TTA Lynx

Cites Work

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• Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code
• Evolution of the genetic code based on conservative changes of codons, amino acids, and aminoacyl tRNA synthetases
• Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons.
• A new look at the statistical model identification

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