ArticleGenome research2024
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 556 papers.
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556 citing papers in PubMed.
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- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Phylogenomic and Comparative Genomic Analyses Reveal Deep Evolutionary Structure and Cryptic Diversity in the GenusInternational journal of molecular sciences · 2026Article
- Draft Genome Assembly and Annotation of a Male Mezayen Dromedary Camel of the Majaheem Type (Animals : an open access journal from MDPI · 2026Article
- Genomic features, metabolism, and biotechnological applications of Candida tropicalis and other non-albicans Candida species.World journal of microbiology & biotechnology · 2026Review
- Comparative Phylogenomics Reveals Conserved Protoilludene Synthase Neighbourhoods and Unevenly Distributed Biosynthetic Gene Cluster Families in Armillaria.Journal of fungi (Basel, Switzerland) · 2026Article
- Draft genome sequences of 12 fungi occurring in cyanobacteria-dominated biotic soil crusts in the Sonoran Desert.Microbiology resource announcements · 2026Article
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- Genome analysis of the glycosphingolipid-producing green alga tetraselmis sp. NKG400013.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- A marine-derived fungal genome of Annulohypoxylon annulatoides reveals AT-rich isochores with putative regulatory functions.G3 (Bethesda, Md.) · 2026Article
- From functional annotation to functional meaning in microbiome research.Environmental microbiome · 2026Review
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Annotated genome assemblies of two temperate North American dung beetles, Canthon chalcites and Phanaeus vindex.G3 (Bethesda, Md.) · 2026Article
- Changes in Alternative Splicing are Associated with Insecticide Response and Resistance.Genome biology and evolution · 2026Article
496 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.