| Publication type: | Book part |
| Type of review: | Editorial review |
| Title: | Visualizing codon usage within and across genomes : concepts and tools |
| Authors: | Ostash, Bohdan Anisimova, Maria |
| et. al: | No |
| DOI: | 10.1007/978-981-15-2445-5_13 |
| Published in: | Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications |
| Editors of the parent work: | Srinivasa, K. G. Siddesh, G. M. Manisekhar, S. R. |
| Page(s): | 213 |
| Pages to: | 288 |
| Issue Date: | 2020 |
| Series: | Algorithms for Intelligent Systems |
| Publisher / Ed. Institution: | Springer |
| Publisher / Ed. Institution: | Singapore |
| ISBN: | 978-981-15-2445-5 978-981-15-2444-8 |
| Language: | English |
| Subjects: | Genetic code; Codon context; Genetics; Evolution; Gene; Sequence analysis |
| Subject (DDC): | 572: Biochemistry |
| Abstract: | Cost and time of genome sequencing have plummeted over the last decade. This leads to explosive growth of genetic databases and development of novel sequencing-based approaches to study various biological phenomena. The database growth was particularly beneficial for investigation of protein-coding sequences at the codon level, requiring the access to large sets of related genomes. Such studies are expected to illuminate biological forces that shape primary structure of coding sequences and predict their evolutionary trajectories more precisely. In addition to fundamental interest, codon usage studies are of ample practical value, for example, in drug discovery and genomic medicine areas. Nevertheless, the depth of our understanding of codon-related issues is currently shallower as compared to what we know about nucleotide and amino acid sequences. Besides the lack of adequate datasets in the early days of molecular biology, codon usage studies, in our opinion, suffer from underdevelopment of easy-to-use tools to analyze and visualize how codon sequence changes along the gene and across the homologous genes in course of evolution. In this review, we aim to describe main areas of codon usage studies with an emphasis on the tools that allow visual interpretation of the data. We discuss underlying principles of different approaches, what kind of statistics lends confidence in their results and what has to be done to further boost the field of codon usage research. |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/19602 |
| Fulltext version: | Published version |
| License (according to publishing contract): | Licence according to publishing contract |
| Departement: | Life Sciences and Facility Management |
| Organisational Unit: | Institute of Computational Life Sciences (ICLS) |
| Published as part of the ZHAW project: | The effect of programmed ribosomal frameshifting on codon usage bias |
| Appears in collections: | Publikationen Life Sciences und Facility Management |
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Ostash, B., & Anisimova, M. (2020). Visualizing codon usage within and across genomes : concepts and tools. In K. G. Srinivasa, G. M. Siddesh, & S. R. Manisekhar (Eds.), Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications (pp. 213–288). Springer. https://doi.org/10.1007/978-981-15-2445-5_13
Ostash, B. and Anisimova, M. (2020) ‘Visualizing codon usage within and across genomes : concepts and tools’, in K.G. Srinivasa, G.M. Siddesh, and S.R. Manisekhar (eds) Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Singapore: Springer, pp. 213–288. Available at: https://doi.org/10.1007/978-981-15-2445-5_13.
B. Ostash and M. Anisimova, “Visualizing codon usage within and across genomes : concepts and tools,” in Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications, K. G. Srinivasa, G. M. Siddesh, and S. R. Manisekhar, Eds. Singapore: Springer, 2020, pp. 213–288. doi: 10.1007/978-981-15-2445-5_13.
OSTASH, Bohdan und Maria ANISIMOVA, 2020. Visualizing codon usage within and across genomes : concepts and tools. In: K. G. SRINIVASA, G. M. SIDDESH und S. R. MANISEKHAR (Hrsg.), Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Singapore: Springer. S. 213–288. ISBN 978-981-15-2445-5
Ostash, Bohdan, and Maria Anisimova. 2020. “Visualizing Codon Usage within and across Genomes : Concepts and Tools.” In Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications, edited by K. G. Srinivasa, G. M. Siddesh, and S. R. Manisekhar, 213–88. Singapore: Springer. https://doi.org/10.1007/978-981-15-2445-5_13.
Ostash, Bohdan, and Maria Anisimova. “Visualizing Codon Usage within and across Genomes : Concepts and Tools.” Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications, edited by K. G. Srinivasa et al., Springer, 2020, pp. 213–88, https://doi.org/10.1007/978-981-15-2445-5_13.
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