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PaTre: a method for Paralogy Trees construction

Pisanti, Nadia and Marangoni, Roberto and Ferragina, Paolo and Frangioni, Antonio and Luccio, Fabrizio and Savona, Antonio (2001) PaTre: a method for Paralogy Trees construction. Technical Report del Dipartimento di Informatica . Università di Pisa, Pisa, IT.

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    Genes belonging to the same organism are called paralogs when they show a significant similarity in the sequences, even if they have a different biological function. It is an emergent biological paradigm that the families of paralogs in a genome derive from a mechanism of iterated gene duplication-with-modification. In order to investigate the evolution of organisms, it can be useful to infer the duplications that have taken place starting from an hypothetical original gene, and that have led to the current paralog genes family. This information can naturally be represented in a paralogy tree. Here we present a method, called PaTre, to generate a paralogy tree from a family of paralog genes. PaTre uses new techniques motivated by the specific application. The reliability of the inferential process is tested by means of a simulator that implements different hypotheses on the duplication-with-modification paradigm, and checked on real data.

    Item Type: Book
    Uncontrolled Keywords: Paralog genes, Paralogy trees, Transformation Distance, Lightest Spanning Arborescence
    Subjects: Area01 - Scienze matematiche e informatiche > INF/01 - Informatica
    Divisions: Dipartimenti (until 2012) > DIPARTIMENTO DI INFORMATICA
    Depositing User: dott.ssa Sandra Faita
    Date Deposited: 22 Dec 2014 14:24
    Last Modified: 22 Dec 2014 14:24
    URI: http://eprints.adm.unipi.it/id/eprint/2064

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