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. Author manuscript; available in PMC: 2020 Jan 1.
Published in final edited form as: Methods Mol Biol. 2019;1962:65–95. doi: 10.1007/978-1-4939-9173-0_5

Figure 2:

Figure 2:

BRAKER pipeline: A) Training GeneMark-ES on genome data only; ab initio gene prediction with AUGUSTUS. B) Training GeneMark-ET supported by RNA-Seq spliced alignment information, prediction with AUGUSTUS with that same spliced alignment information. C) Training GeneMark-EP on protein spliced alignment information, prediction with AUGUSTUS with that same spliced alignment information. D) Training GeneMark-ETP supported by RNA-Seq alignment information and protein spliced alignment information, prediction with AUGUSTUS using the same alignment information. Introns supported by both RNA-Seq and protein alignment information are trusted - their prediction in gene structures by GeneMark-ETP and AUGUSTUS is enforced. Proteins used for C) and D) can be of longer evolutionary distance.