Abstract
Gene prediction in large and highly repetitive grass genomes like barley is complicated by large numbers of transposable elements (TEs), pseudogenes and often incomplete or un-/miss-oriented genomic sequence. In this chapter, we describe the automated gene prediction and annotation pipeline used for the latest barley reference genome sequence, as well as the genomic evidence used to predict gene models. Additional topics cover the (automated) functional annotation, the evaluation of the gene models, and a comprehensive discussion about shortcomings of the current annotation and ways to improve it further.
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Twardziok, S.O. et al. (2018). Gene Prediction in the Barley Genome. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_6
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