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CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition

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Bioinformatics for DNA Sequence Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 537))

Abstract

The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses.

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Acknowledgments

This work was supported in part by the Biophysics and SCR training grants T32GM08759 and T32GM065103 from NIH. CodonExplorer is hosted on the W.M. Keck Foundation Bioinformatics Facility at the University of Colorado, Boulder.

Author information

Authors and Affiliations

  1. Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA

    Jesse Zaneveld & Noboru Sueoka

  2. Department of Computer Science, University of Colorado, Boulder, CO, USA

    Micah Hamady

  3. Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA

    Rob Knight

Authors
  1. Jesse Zaneveld
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  2. Micah Hamady
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  3. Noboru Sueoka
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  4. Rob Knight
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Editor information

Editors and Affiliations

  1. Dept. Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, 36310, Spain

    David Posada

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Zaneveld, J., Hamady, M., Sueoka, N., Knight, R. (2009). CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_10

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  • DOI: https://doi.org/10.1007/978-1-59745-251-9_10

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-910-9

  • Online ISBN: 978-1-59745-251-9

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