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Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes

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Fungal Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1775))

Abstract

The steps needed to computationally predict genes and transcripts in fungal genomes with support from RNA-Seq data are described in detail for three prediction programs: CodingQuarry, BRAKER1, and Harfang. These programs predicted from 86% to 92% (Harfang) of the genes in a manually curated reference set for Aspergillus niger strain NRRL3. Genes with little or no RNA-Seq read coverage were predicted less successfully than genes with adequate coverage.

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Acknowledgments

This work was supported by Genome Canada and Génome Québec.

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Authors and Affiliations

  1. Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada

    Ian Reid

Authors
  1. Ian Reid
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Corresponding author

Correspondence to Ian Reid .

Editor information

Editors and Affiliations

  1. Fungal Physiology, Westerdijk Fungal, Biodiversity Institute, Utrecht, The Netherlands

    Ronald P. de Vries

  2. Centre for Structural and Functional Genomics, Concordia University, Montreal, Québec, Canada

    Adrian Tsang

  3. US Department of Energy, Joint Genome Institute, Walnut Creek, California, USA

    Igor V. Grigoriev

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Reid, I. (2018). Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes. In: de Vries, R., Tsang, A., Grigoriev, I. (eds) Fungal Genomics. Methods in Molecular Biology, vol 1775. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7804-5_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7804-5_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7803-8

  • Online ISBN: 978-1-4939-7804-5

  • eBook Packages: Springer Protocols

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