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Codon Resolution Analysis of Ribosome Profiling Data

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Ribosome Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2252))

Abstract

Translation is a central biological process in living cells. Ribosome profiling approach enables assessing translation on a global, cell-wide level. Extracting versatile information from the ribosome profiling data usually requires specialized expertise for handling the sequencing data that is not available to the broad community of experimentalists. Here, we provide an easy-to-use and modifiable workflow that uses a small set of commands and enables full data analysis in a standardized way, including precise positioning of the ribosome-protected fragments, for determining codon-specific translation features. The workflow is complemented with simple step-by-step explanations and is accessible to scientists with no computational background.

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Acknowledgments

The work was supported by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 764591 (SynCrop) and by Deutsche Forschungsgemeinschaft SPP2002 (IG 73/16-1) grants to Z.I.

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Authors and Affiliations

  1. GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany

    Alexander Bartholomäus

  2. Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany

    Zoya Ignatova

Authors
  1. Alexander Bartholomäus
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  2. Zoya Ignatova
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Corresponding author

Correspondence to Zoya Ignatova .

Editor information

Editors and Affiliations

  1. Department of Dermatology, Boston University School of Medicine, Boston, MA, USA

    Vyacheslav M. Labunskyy

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Bartholomäus, A., Ignatova, Z. (2021). Codon Resolution Analysis of Ribosome Profiling Data. In: Labunskyy, V.M. (eds) Ribosome Profiling. Methods in Molecular Biology, vol 2252. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1150-0_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1150-0_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1149-4

  • Online ISBN: 978-1-0716-1150-0

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