BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

2021/01/06 by Tomáš Brůna, Katharina J. Hoff, Alexandre Lomsadze +2 · 99 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Phytoplasmas and Hemiptera pathogens #RNA and protein synthesis mechanisms

paper · pdf · doi:10.1093/nargab/lqaa108

openalex publication_date 2021/01/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

The task of eukaryotic genome annotation remains challenging. Only a few genomes could serve as standards of annotation achieved through a tremendous investment of human curation efforts. Still, the correctness of all alternative isoforms, even in the best-annotated genomes, could be a good subject for further investigation. The new BRAKER2 pipeline generates and integrates external protein support into the iterative process of training and gene prediction by GeneMark-EP+ and AUGUSTUS. BRAKER2 continues the line started by BRAKER1 where self-training GeneMark-ET and AUGUSTUS made gene predictions supported by transcriptomic data. Among the challenges addressed by the new pipeline was a generation of reliable hints to protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. In comparison with other pipelines for eukaryotic genome annotation, BRAKER2 is fully automatic. It is favorably compared under equal conditions with other pipelines, e.g. MAKER2, in terms of accuracy and performance. Development of BRAKER2 should facilitate solving the task of harmonization of annotation of protein-coding genes in genomes of different eukaryotic species. However, we fully understand that several more innovations are needed in transcriptomic and proteomic technologies as well as in algorithmic development to reach the goal of highly accurate annotation of eukaryotic genomes.

Citations

• Gene identification in novel eukaryotic genomes by self-training algorithm
• BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

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