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Updated: Feb 9, 2026
Molecular Entanglement and Electrospinnability of Biopolymers
Published on: September 3, 2014
KnotGenome: a server to analyze entanglements of chromosomes
Joanna I Sulkowska1,2, Szymon Niewieczerzal1, Aleksandra I Jarmolinska1,3
1Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
Abstract:
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome 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 determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromosomes are presented graphically in an intuitive way. It is also possible to relax structure with short molecular dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu.pl/.
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