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

By Tomás Bruna, Katharina Jasmin Hoff, Alexandre Lomsadze, Mario Stanke, Mark Borodovsky. bioRxiv, 2020

1,454 citations recorded by the source corpus.

Full automation of gene prediction has become an important bioinformatics task since the advent of next generation sequencing. The eukaryotic genome annotation pipeline BRAKER1 had combined self-training GeneMark-ET with AUGUSTUS to generate genes’ coordinates with support of transcriptomic data. Here, we introduce BRAKER2, a pipeline with GeneMark-EP+ and AUGUSTUS externally supported by cross-species protein sequences aligned to the genome. Among the challenges addressed in the development of the new pipeline was generation of reliable hints to the locations of protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. Under equal conditions, the gene prediction accuracy of BRAKER2 was shown to be higher than the one of MAKER2, yet another genome annotation pipeline. Also, in comparison with BRAKER1 supported by a large volume of transcript data, BRAKER2 could produce a better gene prediction accuracy if the evolutionary distances to the reference species in the protein database were rather small. All over, our tests demonstrated that fully automatic BRAKER2 is a fast and accurate method for structural annotation of novel eukaryotic genomes.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/17457c97c9c792f0db271cdf7c7c26759d132db1

How researchers see this paper

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In Molecular Biology

1. Mark Borodovsky
2. Alexandre Lomsadze
3. Tomás Bruna
4. Katharina Jasmin Hoff
5. Mario Stanke
6. L. Gabriel
7. Matthis Ebel
8. Fiona Cunningham

In Plant Science

1. Mario Stanke
2. Katharina Jasmin Hoff
3. Mark Borodovsky
4. Alexandre Lomsadze
5. Toby Hunt
6. Paul Flicek

Citations in the corpus

• Ensembl 2023 (2022, methodology): “Protein data from both UniProt and OrthoDB (31) is used to help provide hints to guide BRAKER2.”
• BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, positive): “Earlier developed BRAKER1 (Hoff et al., 2016) and BRAKER2 (Br˚una et al., 2021) combined Gene-30 Mark and AUGUSTUS to utilize, respectively, a single source of extrinsic evidence, either RNA-seq short reads or homologous proteins.”