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Navigating the CoGe Online Software Suite for Polyploidy Research

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Polyploidy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2545))

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Abstract

The CoGe software suite at genomevolution.org hosts a number of tools that facilitate genomic research on plant and animal whole-genome multiplication—polyploidy. SynMap permits analysis and visualization of two-way syntenic dotplot alignments of genomes, includes many options and data/graphics download possibilities, and even permits three-genome synteny maps and interactive views. FractBias is a tool that operates within SynMap that permits calculation and graphic display of genome fragments (such as chromosomes) of one species mapped to another, displaying both blockwise homology depths and the extent of syntenic gene (syntelog) loss following polyploidy events. SynMap macrosynteny results can segue into the microsynteny tool GEvo, which provides genome-browser-like views of homologous genome blocks. CoGe FeatView allows call-up of given gene features already stored in the CoGe resource, and CoGeBlast permits searches for additional features that can be analyzed or downloaded further. Links from these tools can be fed into SynFind, which can find syntenic blocks surrounding a feature across multiple specified genomes while also simultaneously providing overall genome-wide syntenic depth calculations that can be interpreted to reflect polyploidy levels. Here, we describe basic use of these tools on the CoGe software suite.

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Authors and Affiliations

  1. Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA

    Victor A. Albert & Trevor J. Krabbenhoft

Authors
  1. Victor A. Albert
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  2. Trevor J. Krabbenhoft
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Correspondence to Victor A. Albert .

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Editors and Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Albert, V.A., Krabbenhoft, T.J. (2023). Navigating the CoGe Online Software Suite for Polyploidy Research. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_2

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  • DOI: https://doi.org/10.1007/978-1-0716-2561-3_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2560-6

  • Online ISBN: 978-1-0716-2561-3

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