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:
topological mechanisms of action of enzymes such as type II
topisomerases and site-specific recombinases
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)
