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The Incompatible Desiderata of Gene Cluster Properties

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Comparative Genomics (RCG 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3678))

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Abstract

There is widespread interest in comparative genomics in determining if historically and/or functionally related genes are spatially clustered in the genome, and whether the same sets of genes reappear in clusters in two or more genomes. We formalize and analyze the desirable properties of gene clusters and cluster definitions. Through detailed analysis of two commonly applied types of cluster, r-windows and max-gap, we investigate the extent to which a single definition can embody all of these properties simultaneously. We show that many of the most important properties are difficult to satisfy within the same definition. We also examine whether one commonly assumed property, which we call nestedness, is satisfied by the structures present in real genomic data.

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Author information

Authors and Affiliations

  1. Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA

    Rose Hoberman

  2. Departments of Biological Sciences and Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA

    Dannie Durand

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  1. Rose Hoberman
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  2. Dannie Durand
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Editor information

Editors and Affiliations

  1. University of Dublin, Smurfit Institute of Genetics, Trinity College, Ireland

    Aoife McLysaght

  2. Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany

    Daniel H. Huson

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© 2005 Springer-Verlag Berlin Heidelberg

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Hoberman, R., Durand, D. (2005). The Incompatible Desiderata of Gene Cluster Properties. In: McLysaght, A., Huson, D.H. (eds) Comparative Genomics. RCG 2005. Lecture Notes in Computer Science(), vol 3678. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11554714_7

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  • DOI: https://doi.org/10.1007/11554714_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28932-6

  • Online ISBN: 978-3-540-31814-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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