The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
Whole-Genome Annotation with BRAKER
Open accessAbstract
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.
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Cited by
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Ancient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
TSEBRA: transcript selector for BRAKER
Gabriel, L., Hoff, K. J., Brůna, T., Borodovsky, M., & Stanke, M. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04482-0 · Cited by 410
Self-citationYang, T., Liu, R., Luo, Y., Hu, S., Wang, D., Wang, C., Pandey, M. K., Ge, S., Xu, Q., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01172-2 · Cited by 191
Whole-genome analysis of giraffe supports four distinct species
Coimbra, R. T. F., Winter, S., Kumar, V., Koepfli, K.-P., Gooley, R. M., Dobrynin, P., Fennessy, J., & Janke, A. (2021) · Current Biology · doi:10.1016/j.cub.2021.04.033 · Cited by 102
Metadata
- Authors
- Hoff, K. J., Lomsadze, A., Borodovsky, M., & Stanke, M.
- Venue
- Methods in Molecular Biology
- Publisher
- Springer New York
- Published
- 2019
- Volume
- 1962
- Pages
- 65-95
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2941629467
- Cited by
- 719
- References
- 41
- FWCI
- 79.76
- Type
- book chapter
- Language
- en
- Open access
- green
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