BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
By Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke. Bioinform., 2016
1,039 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/34ce19d2e987a2862c7c9bd1c1139ce44dd8593d
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Mark Borodovsky
- Tomás Bruna
- Alexandre Lomsadze
- Katharina Jasmin Hoff
- Mario Stanke
- L. Gabriel
- Matthis Ebel
- Jan Grau
Citations in the corpus
- Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi (2017, background): “Based on this observation, we agree that combined gene prediction pipelines benefit from the inclusion of all available evidence and that performance is decreased if some important evidence is missed (Holt and Yandell, 2011).”
- 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.”
- BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, methodology): “1 Running BRAKER1 BRAKER1 [11] was run with the following command:”
- GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, positive): “When external information representing alternative isoforms is provided at RNA level, an earlier developed pipeline, BRAKER1 (31), uses GeneMark-ET and AUGUSTUS to make predictions of alternative isoforms.”
- Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, background): “…(Salamov and Solovyev, 2000) N/A GenomeScan (Yeh et al., 2001) http://genes.mit.edu/genomescan/ BRAKER1 (Hoff et al., 2016) http://bioinf.uni-greifswald.de/bioinf/braker/ CasFinder N/A http://arep.med.harvard.edu/CasFinder STAR alignment software…”