Whole-Genome Annotation with BRAKER
Whole-Genome Annotation with BRAKER
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DOI：
10.1007/978-1-4939-9173-0_5
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发表时间：
2019-01-01
期刊：
影响因子：
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通讯作者：
Stanke, Mario
中科院分区：
文献类型：
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作者：
Hoff, Katharina J.;Lomsadze, Alexandre;Stanke, Mario
BRAKER是一个在新的真核基因组中进行高度准确和全自动基因预测的管道。它结合了两个主要工具：GeneMark-ES/ET和AUGUSTUS。GeneMark-ES/ET以完全自动化的方式从新的基因组序列中学习其参数;如果可用，它使用外部证据进行模型优化。从GeneMark-ES/ET预测的蛋白质编码基因中，我们选择了一组用于训练AUGUSTUS，AUGUSTUS是最准确的基因发现工具之一，与GeneMark-ES/ET相反，它将外部证据集成到基因预测步骤中。第一个发布的版本BRAKER 1将未组装的RNA-Seq读数的基因组足迹整合到训练和预测步骤中。该管道已扩展到映射的跨物种蛋白质的数据的整合，并使用异质性外在证据，RNA测序和蛋白质比对。在本书的这一章中，我们简要总结了管道方法，并描述了如何在以各种外部证据组合为特征的环境中应用BRAKER。
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.