6533b7d0fe1ef96bd125afab
RESEARCH PRODUCT
KnotGenome: a server to analyze entanglements of chromosomes.
Peter VirnauWanda NiemyskaSzymon NiewieczerzalJoanna I. SulkowskaAleksandra I. JarmolinskaJonathan Tammo Siebertsubject
0301 basic medicinePolynomialProtein ConformationGaussianPolynucleotidesBiologyType (model theory)Molecular Dynamics SimulationPrime (order theory)ChromosomesQuantitative Biology::Subcellular Processes03 medical and health sciencessymbols.namesakeMatrix (mathematics)Knot (unit)Chain (algebraic topology)GeneticsDiscrete mathematicsInternetDiagramComputational BiologyMathematics::Geometric TopologyQuantitative Biology::Genomics030104 developmental biologyWeb Server IssuesymbolsAlgorithmsSoftwaredescription
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/.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2018-03-26 | Nucleic acids research |