BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

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ID: 296596
2015
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Abstract
Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step.BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/katharina.hoff@uni-greifswald.de or borodovsky@gatech.eduSupplementary data are available at Bioinformatics online.
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openalex_W2216234219 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Katharina J. Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
Journal BMC Bioinformatics
Year 2015
DOI
10.1093/bioinformatics/btv661
URL
https://academic.oup.com/bioinformatics/article-pdf/32/5/767/25588988/btv661.pdf
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