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Improving Re-annotation of Annotated Eukaryotic Genomes

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Big Data Analytics in Genomics

Abstract

In the age of post-genomics, the task of improving existing annotation is one of the major challenge. The sequenced transcriptome allows to revisit the annotated sequenced genome of the corresponding organism and improve the existing gene models. In addition, misleading annotations propagate in multiple databases by comparative approaches of annotation, automatic annotation, and lack of curating power in the face of large data volume. In this pursuit, re-annotated improved gene models can prevent misleading structural and functional annotation of genes and proteins. In this chapter, we will highlight annotation and re-annotation procedures and will explain how annotations can be improved using computational methods. Our integrative workflow can be used to re-annotate genomes of any sequenced eukaryotic organism. We describe the annotation of splice sites, open reading frames, encoded proteins and peptides, hints for functional annotation including phylogenetic and domain analysis as well as critical evaluation of data transfer procedures, and the genome annotation process.

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    Authors and Affiliations

    1. Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Wuerzburg, Germany

      Shishir K. Gupta, Elena Bencurova, Mugdha Srivastava, Pirasteh Pahlavan, Johannes Balkenhol & Thomas Dandekar

    2. Department of Microbiology, Biocenter, University of Würzburg, Am Hubland, 97074, Wuerzburg, Germany

      Shishir K. Gupta

    3. University of Veterinary Medicine and Pharmacy, Komenskeho 73, Kosice, 04181, Slovakia

      Elena Bencurova

    4. Leibniz-Institute, German Collection of Microorganisms and Cell Cultures Gmbh, Braunschweig, Germany

      Pirasteh Pahlavan

    5. EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany

      Thomas Dandekar

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    1. Shishir K. Gupta
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    1. Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong

      Ka-Chun Wong

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    Gupta, S.K., Bencurova, E., Srivastava, M., Pahlavan, P., Balkenhol, J., Dandekar, T. (2016). Improving Re-annotation of Annotated Eukaryotic Genomes. In: Wong, KC. (eds) Big Data Analytics in Genomics. Springer, Cham. https://doi.org/10.1007/978-3-319-41279-5_5

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