The rapidly growing number of sequenced genomes requires fully automated methods for accurate gene structure annotation. With this goal in mind, we have developed BRAKER1, a combination of GeneMark-ET and AUGUSTUS that uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome.
However, the quality of RNA-Seq data that is available for annotating a novel genome is variable, and in some cases, RNA-Seq data is not available, at all.
BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
In contrast to other available methods that rely on protein homology information, BRAKER2 reaches high gene prediction accuracy even in the absence of the annotation of very closely related species and in the absence of RNA-Seq data.
Publications
Brůna, T., Hoff, K.J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2020). BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database, NAR Genomics and Bioinformatics 3(1):lqaa108, doi: 10.1093/nargab/lqaa108.
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M (2019). Whole-Genome Annotation with BRAKER. Methods Mol Biol. 1962:65-95.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M (2016). BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics, 32(5):767-769.
Stanke M, Diekhans M, Baertsch, R. and Haussler D (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics.
Stanke M, Schöffmann O, Morgenstern, B, Waack S (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62.
Licenses
BRAKER: Artistic
Augustus: Artistic
BAMTools: MIT
HTSLIB: MIT/Expat
BCFTools: MIT/Expat
SamTools: MIT/Expat
GeneMark: Own license, free for academic use
GenomeThreader: ISC
