KnotGenome: a server to analyze entanglements of chromosomes

The KnotGenome server enables the topological analysis of chromosome model data using three- dimensional coordinate files of chromosomes as in- put. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chro- mosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are de- termined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromo- somes are presented graphically in an intuitive way. It is also possible to relax structure with short molecu- lar dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu. pl/.