ArticleMethods in molecular biology (Clifton, N.J.)2019
Whole-Genome Annotation with BRAKER.
Article in Methods in molecular biology (Clifton, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 476 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
476 citing papers in PubMed.
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- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Telomere-to-Telomere Genome Assembly ofJournal of fungi (Basel, Switzerland) · 2026Article
- Gene regulation in response to host sex and infection route in Brugia pahangi with new genome annotation.G3 (Bethesda, Md.) · 2026Article
- Genomic Insights Into the Evolution of Parental Care in Weevils.Genome biology and evolution · 2026Article
- A chromosome-level genome assembly of Solanum brevicaule (PI 473011) Y1-5, a wild potato relative with robust resistance to potato cyst nematodes.The plant genome · 2026Article
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- Engineering carotenoid and steroidal glycoalkaloid depleted tomato fruit for heterologous production of high value terpenes.bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic responses in ham mite (Tyrophagus putrescentiae) to propylene glycol exposure.Scientific reports · 2026Article
- Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in Submergence-Tolerant Rice Varieties.Rice (New York, N.Y.) · 2026Article
- Draft genome sequence of the peptaibol producerMicrobiology resource announcements · 2026Article
- Assembled and annotated reference genome and demographic history of the eastern chipmunk (Tamias striatus).Molecular genetics and genomics : MGG · 2026Article
416 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
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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Registered trials
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