TopoICE and other software tools for investigating topological problems in DNA
Seminar Room 1, Newton Institute
AbstractMathematicians and biologists studying knotting and tangling issues in DNA can benefit from powerful interactive software tools. These can be used to explore what is mathematically possibly in certain kinds of reactions that DNA may undergo (crossing changes or recombination, for example). This information may be helpful in refining biological models or even in suggesting new experiments. In this talk, we will examine several software tools starting with the Topological Interactive Construction Engine (TopoICE). TopoICE has been available as part of the KnotPlot package for several years, in two versions: TopoICE-X (crossing changes) and TopoICE-R (recombination). Here we present these in a revamped, extended and more usable form. Also, we introduce TopoICE-S, intended to investigate knot distances via smoothings. This will be accompanied by newly obtained smoothing distance information. This talk will also unveil TopoICE and other DNA topology tools as free standalone applications (independent of KnotPlot) and running on mobile devices. This is joint work with Isabel Darcy.
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