Whole-Genome Annotation with BRAKER

• Type of Material: Article
• Authors: Katharina Hoff, Ernst Moritz Arndt Universitat Greifswald; Alexandre Lomsadze, Georgia Tech; Mark Borodovsky, Emory University; Mario Stanke, Ernst Moritz Arndt Universitat Greifswald
• Language: English
• Date: 2019-01-01
• Publisher: HUMANA PRESS INC
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © Springer Science+Business Media, LLC, part of Springer Nature 2019.
• Final Published Version (URL): http://dx.doi.org/10.1007/978-1-4939-9173-0_5
• Title of Journal or Parent Work: GENE PREDICTION: METHODS AND PROTOCOLS
• Volume: 1962
• Start Page: 65
• End Page: 95
• Grant/Funding Information: This work is supported in part by the US National Institutes of Health grant HG000783 to MB and by German Research Foundation grant 1009/12–1 to MS.
• Keywords: BRAKER; AUGUSTUS; SEQUENCES; ALIGNMENT; Gene prediction; Science & Technology; RNA-Seq reads; Life Sciences & Biomedicine; Biochemical Research Methods; Biochemistry & Molecular Biology; FUNGAL; PREDICTION; Protein mapping to genome; IDENTIFICATION; GeneMark-ES/ET; Genome annotation pipeline; Protein-coding genes
• Research Categories: Chemistry, Biochemistry; Biology, Cell; Biology, Genetics; Health Sciences, Epidemiology

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.