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Predicting Genes in Closely Related Species with Scipio and WebScipio

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Book cover Gene Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1962))

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Abstract

Scipio and WebScipio are homology-based gene prediction software designed for annotating multigenic families and for transferring annotations from one species to closely related species. The strengths include the power to cope with sequencing-related problems such as sequencing errors and assemblies with short contigs but also the ability to correctly predict genes with unusually long introns and/or rather short exons. WebScipio is connected to diArk, the largest collection of eukaryotic genome assemblies, and thereby offers a very convenient way to correct existing annotations and to extend protein family datasets. WebScipio is also a key resource for researchers interested in mutually exclusive splicing, allowing to search for alternative exons not only in introns but also in up- and downstream regions in case of incompleteness of the search sequence. In this chapter, I describe how to use Scipio and WebScipio keeping a first-time user in mind.

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Authors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany

    Martin Kollmar

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  1. Martin Kollmar
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Correspondence to Martin Kollmar .

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Editors and Affiliations

  1. Group Systems Biology of Motor Proteins, Department NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany

    Martin Kollmar

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Kollmar, M. (2019). Predicting Genes in Closely Related Species with Scipio and WebScipio. In: Kollmar, M. (eds) Gene Prediction. Methods in Molecular Biology, vol 1962. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9173-0_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9173-0_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9172-3

  • Online ISBN: 978-1-4939-9173-0

  • eBook Packages: Springer Protocols

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