AI Article Synopsis

  • The KnotGenome server analyzes the topology of chromosome models using 3D coordinate files to identify prime and composite knots within single chromosomes and connections between them.
  • It provides a visual representation of knotting complexity through a matrix diagram, showing the knot types of both the complete polynucleotide chain and its subchains.
  • Users can also perform short molecular dynamics runs to relax the chromosome structure before analysis, and the server is freely accessible online at http://knotgenom.cent.uw.edu.pl/.

Article 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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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030981PMC
http://dx.doi.org/10.1093/nar/gky511DOI Listing

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