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

Katharina J. Hoff | Zendy; Simone Lange | Zendy; Alexandre Lomsadze | Zendy; Mark Borodovsky | Zendy; Mario Stanke | Zendy

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

Author(s) -

Katharina J. Hoff,

Simone Lange,

Alexandre Lomsadze,

Mark Borodovsky,

Mario Stanke

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv661

Subject(s) - annotation , gene annotation , computer science , pipeline (software) , genome , genome project , gene prediction , set (abstract data type) , computational biology , rna seq , data mining , gene , artificial intelligence , biology , genetics , transcriptome , gene expression , programming language

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.

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