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Sistema Automatizado para Simular la Electroforesis de Campo Pulsante y Almacenar los Pulsotipos virtuales del Genoma Bacteriano

  • E. PlasenciaEmail author
  • Y. Cárdenas
  • L. López-Cánovas
  • A. M. Riverón
Part of the IFMBE Proceedings book series (IFMBE, volume 33)

Abstract

Pulsed-field gel electrophoresis (PFGE) is a method for separating DNA molecules under the action of two alternating electric fields. This methodology separates chromosomal sized DNA molecules in an agarose gel as band patterns. The Department of Molecular Biology of the Cuban Neurosciences Center developed in 1997 a miniaturized PFGE equipment named Guefast. This enables the comparison of the genome of different clinical bacterial isolates, providing information on the similarity between these isolates and facilitating the determination of the genetic relationship between them. In this work Guefast system capabilities were expanded, incorporating an electrophoresis simulator. The software stores a set of conditions of experimental electrophoretic run and of restriction enzymes that recognize the bacterial DNA sub-sequences and cleave them into the recognition site. Using this information, the software uses the equations describing the migration of DNA molecules in a gel of agarose to simulate the band patterns that would be obtained in an experimental electrophoretic run. These band patterns are encoded as vectors with binary attributes, where “1” represents the presence of band and “0” the absence of a band in each coordinate of the migration path along the virtual gel. This information is centrally stored in a database, which facilitates the exchange of results among Department researchers.

Palabras claves

Pulsed field gel electrophoresis simulation DNA band pattern 

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Copyright information

© Springer Berlin Heidelberg 2013

Authors and Affiliations

  • E. Plasencia
    • 1
    Email author
  • Y. Cárdenas
    • 1
  • L. López-Cánovas
    • 1
  • A. M. Riverón
    • 1
  1. 1.Biología MolecularCentro de Neurociencias de CubaLa HabanaCuba

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