What question did this study set out to answer?

To develop and evaluate BRAKER2, a fully automated pipeline integrating external protein database support into GeneMark-EP+ and AUGUSTUS for eukaryotic genome annotation.

January 6, 2021NAR Genomics and BioinformaticsOpen Access

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

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Authors

TBTomáš BrůnaLawrence Berkeley National Laboratory KHKatharina J. HoffUniversitätsmedizin Greifswald ALAlexandre LomsadzeThe Wallace H. Coulter Department of Biomedical Engineering

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Implication

Algorithm validation study reveals automated, accurate gene prediction in eukaryotic genomes using protein database support, indicating improved annotation across diverse species.

Key Points

To develop and evaluate BRAKER2, a fully automated pipeline integrating external protein database support into GeneMark-EP+ and AUGUSTUS for eukaryotic genome annotation.
Integrated external homologous protein support into an iterative training and gene prediction pipeline linking GeneMark-EP+ and AUGUSTUS.
Engineered methods to derive reliable hints for protein-coding exon boundaries from evolutionarily distant homologous proteins.
Benchmarked annotation accuracy and computational performance against established tools, including MAKER2, under standardized test conditions.
Achieved a fully automatic pipeline for eukaryotic genome annotation that eliminates the need for manual curation.
Demonstrated favorable accuracy and performance comparisons when evaluated against the MAKER2 annotation pipeline under equal conditions.

Cite This Study

Brůna et al. (2021) studied this question.

synapsesocial.com/papers/69d6b4cefca0359822aa819a https://doi.org/10.1093/nargab/lqaa108

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Implication

Algorithm validation study reveals automated, accurate gene prediction in eukaryotic genomes using protein database support, indicating improved annotation across diverse species.

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

Discussion

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Implication

Key Points

Cite This Study

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

Discussion

Member takes

Implication

Key Points

Cite This Study

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