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Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)

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Brachypodium Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1667))

Abstract

One amino acid is added to a growing peptide by a ribosome through reading triple nucleotides, i.e., a codon, each time. Twenty species of amino acids are often coded by 61 codons, so one amino acid can be coded by more than one codon and the codons coding the same amino acid are called synonymous. Intriguingly, synonymous codons’ usage is often uneven: some are used more often than their alternatives in a genome. The unevenness of codon usage is termed codon usage bias (CUB). CUB is widespread, and its causes and consequences have been under intensive investigation. To facilitate the studying of CUB, in this chapter we present a protocol of estimating CUB by using the free software Codon Usage Analyzer, and apply it to Brachypodium distachyon as an example. To accomplish this protocol, the readers need some basic command-line skills. Briefly, the protocol comprises four major steps: downloading data and software, setting up computing environment, preparing data, and estimating CUB.

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Acknowledgement

ZZ is grateful to Dr. Daven C Presgraves for the strong support in ZZ’s research.

Author information

Authors and Affiliations

  1. Department of Biology, University of Rochester, River Campus Box 270211, Rochester, NY, 14627, USA

    Zhenguo Zhang

  2. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, 380010, Italy

    Gaurav Sablok

  3. Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia

    Gaurav Sablok

Authors
  1. Zhenguo Zhang
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  2. Gaurav Sablok
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Corresponding author

Correspondence to Zhenguo Zhang .

Editor information

Editors and Affiliations

  1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

    Gaurav Sablok

  2. Sabanci University, Istanbul, Turkey

    Hikmet Budak

  3. Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales, Australia

    Peter J. Ralph

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Zhang, Z., Sablok, G. (2018). Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA). In: Sablok, G., Budak, H., Ralph, P. (eds) Brachypodium Genomics. Methods in Molecular Biology, vol 1667. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7278-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7278-4_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7276-0

  • Online ISBN: 978-1-4939-7278-4

  • eBook Packages: Springer Protocols

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