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A genome analysis based on repeat sharing gene networks

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Abstract

Motivated by an interest to understand how information is organized within genomes, and how genes communicate between each other in the transcription process, in this paper we propose a novel network based methodology for genomic sequence analysis, specifically applied to three organisms: Nanoarchaeum equitans, Escherichia coli, and Saccaromyces cerevisiae. A dictionary based approach previously introduced is here continued through a repeat analysis in genic and intergenic regions. Key results of this work have been found in a biological and computational analysis of novel parametrized gene networks, defined by means of motifs of fixed length occurring inside multiple genes. Cliques emerge as groups of genes sharing a long repeat with a clear biological interpretation, while a (complete, paralog) cluster analysis has outlined some unexpected regularity. Repeat sharing gene networks may be applied in contexts of comparative genomics, as an investigation methodology for a comprehension of evolutional and functional properties of genes.

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Notes

  1. www.cbmc.it/external/Infogenomics3.

  2. For example, capability of a protein to break chemical bonds or phosphorilate another protein.

  3. For example, a protein involved in replication, energy production or movement.

  4. Localization of the protein, for example in nucleus, on membranes, in ribosomes.

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Acknowledgments

The first author has been financially supported by CBMC (Center for Biomedical Computing), in Verona, Italy, which also provided us with the server where all the computations were performed. All the authors are grateful for numerous and detailed improvements suggested by anonymous referees, and inspiring discussions on Infogenomic approach with V. Manca.

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Authors and Affiliations

  1. Department of Computer Science, Verona University, Strada Le Grazie 15, 37134, Verona, Italy

    Alberto Castellini, Giuditta Franco & Alessio Milanese

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  1. Alberto Castellini
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  2. Giuditta Franco
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  3. Alessio Milanese
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Correspondence to Alberto Castellini.

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Castellini, A., Franco, G. & Milanese, A. A genome analysis based on repeat sharing gene networks. Nat Comput 14, 403–420 (2015). https://doi.org/10.1007/s11047-014-9437-6

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