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KnotGenome: a server to analyze entanglements of chromosomes.
Sulkowska, Joanna I; Niewieczerzal, Szymon; Jarmolinska, Aleksandra I; Siebert, Jonathan T; Virnau, Peter; Niemyska, Wanda.
Affiliation
  • Sulkowska JI; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
  • Niewieczerzal S; Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
  • Jarmolinska AI; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
  • Siebert JT; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
  • Virnau P; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
  • Niemyska W; Johannes Gutenberg-Universität Mainz, Institut für Physik, Staudingerweg 9, Mainz, 55128, Germany.
Nucleic Acids Res ; 46(W1): W17-W24, 2018 07 02.
Article in En | MEDLINE | ID: mdl-29905836
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Chromosomes / Computational Biology / Internet Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country: Poland Country of publication: United kingdom
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Chromosomes / Computational Biology / Internet Language: En Journal: Nucleic Acids Res Year: 2018 Document type: Article Affiliation country: Poland Country of publication: United kingdom