Mariel Vazquez 

Image: Photos of SF State students and scenes from around campus

Software

  • TangleSolve (paper) is a Java applet which implements the tangle method for site-specific recombination. TangleSolve offers an easy to use graphical user interface for analyzing and vizualizing site-specific recombination mechanisms.

  • Other software
              • DNA Toplogy  
        The Arsuaga and Vazquez research groups have developed a series of computational tools to         model polygonial chains in 3-dimensional space (on and off-lattice) and to explore their                          conformation space (e.g. BFACF, crankshaft, Hedgehog). We are interested in the following                 problems:
      1. properties of circular chains in confinement (e.g. DNA packing in bacteriophages, formation of the trynanosome mini-circle network);
      2. topological mechanisms of action of enzymes such as type II topisomerases and site-specific recombinases.
      3. topological identification of DNA knots (using gauss codes, Dowker codes, polynomial invariants)

Please contact Mariel or Javier for details, and for access to data and/or software. Several of the tools were developed by Rob Scharein and can be interfaced to work within Knotplot.

  • Chromosome Positioning
On a separate line of research, in collaboration with the Arsuaga group we have developed software to study intermingling of chromosomes in the cell nucleus, as well as an applet to analyze pairwise interactions between chromosomes (SCHIP, developed jointly with Sergi Vives, paper)
             Related software developed in Rainen Sach's group can be found at this site
  • Computational Homology and cancer
            Finally we have also worked an application of computational Homology to analyze genomic             data from cancer patients (see Javier Arsuaga's description and images)



 


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