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Whole-Genome Annotation with BRAKER

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Gene Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1962))

Abstract

BRAKER is a pipeline for highly accurate and fully automated gene prediction in novel eukaryotic genomes. It combines two major tools: GeneMark-ES/ET and AUGUSTUS. GeneMark-ES/ET learns its parameters from a novel genomic sequence in a fully automated fashion; if available, it uses extrinsic evidence for model refinement. From the protein-coding genes predicted by GeneMark-ES/ET, we select a set for training AUGUSTUS, one of the most accurate gene finding tools that, in contrast to GeneMark-ES/ET, integrates extrinsic evidence already into the gene prediction step. The first published version, BRAKER1, integrated genomic footprints of unassembled RNA-Seq reads into the training as well as into the prediction steps. The pipeline has since been extended to the integration of data on mapped cross-species proteins, and to the usage of heterogeneous extrinsic evidence, both RNA-Seq and protein alignments. In this book chapter, we briefly summarize the pipeline methodology and describe how to apply BRAKER in environments characterized by various combinations of external evidence.

The authors “Alexandre Lomsadze”, “Mark Borodovsky”, and “Mario Stanke” contributed equally.

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Acknowledgements

This work is supported in part by the US National Institutes of Health grant HG000783 to MB, by the German Research Foundation grant 1009/12-1 to MS and by the US National Institutes of Health grant GM128145 to MB and MS.

Author information

Authors and Affiliations

  1. University of Greifswald, Institute of Mathematics and Computer Science, Greifswald, Germany

    Katharina J. Hoff & Mario Stanke

  2. Joint Georgia Tech and Emory University Wallace H Coulter Department of Biomedical Engineering, Atlanta, GA, USA

    Alexandre Lomsadze & Mark Borodovsky

  3. School of Computational Science and Engineering, Atlanta, GA, 30332, USA

    Mark Borodovsky

  4. Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia

    Mark Borodovsky

Authors
  1. Katharina J. Hoff
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  2. Alexandre Lomsadze
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  3. Mark Borodovsky
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  4. Mario Stanke
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Corresponding authors

Correspondence to Katharina J. Hoff or Mark Borodovsky .

Editor information

Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany

    Martin Kollmar

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Hoff, K.J., Lomsadze, A., Borodovsky, M., Stanke, M. (2019). Whole-Genome Annotation with BRAKER. In: Kollmar, M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9173-0_5

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  • DOI: https://doi.org/10.1007/978-1-4939-9173-0_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9172-3

  • Online ISBN: 978-1-4939-9173-0

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