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 input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is pre...

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Autores principales: Sulkowska, Joanna I, Niewieczerzal, Szymon, Jarmolinska, Aleksandra I, Siebert, Jonathan T, Virnau, Peter, Niemyska, Wanda
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Web Server Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030981/
https://www.ncbi.nlm.nih.gov/pubmed/29905836
http://dx.doi.org/10.1093/nar/gky511
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author Sulkowska, Joanna I
Niewieczerzal, Szymon
Jarmolinska, Aleksandra I
Siebert, Jonathan T
Virnau, Peter
Niemyska, Wanda
author_facet Sulkowska, Joanna I
Niewieczerzal, Szymon
Jarmolinska, Aleksandra I
Siebert, Jonathan T
Virnau, Peter
Niemyska, Wanda
author_sort Sulkowska, Joanna I
collection PubMed
description 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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spelling pubmed-60309812018-07-10 KnotGenome: a server to analyze entanglements of chromosomes Sulkowska, Joanna I Niewieczerzal, Szymon Jarmolinska, Aleksandra I Siebert, Jonathan T Virnau, Peter Niemyska, Wanda Nucleic Acids Res Web Server Issue 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/. Oxford University Press 2018-07-02 2018-06-14 /pmc/articles/PMC6030981/ /pubmed/29905836 http://dx.doi.org/10.1093/nar/gky511 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Sulkowska, Joanna I
Niewieczerzal, Szymon
Jarmolinska, Aleksandra I
Siebert, Jonathan T
Virnau, Peter
Niemyska, Wanda
KnotGenome: a server to analyze entanglements of chromosomes
title KnotGenome: a server to analyze entanglements of chromosomes
title_full KnotGenome: a server to analyze entanglements of chromosomes
title_fullStr KnotGenome: a server to analyze entanglements of chromosomes
title_full_unstemmed KnotGenome: a server to analyze entanglements of chromosomes
title_short KnotGenome: a server to analyze entanglements of chromosomes
title_sort knotgenome: a server to analyze entanglements of chromosomes
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030981/
https://www.ncbi.nlm.nih.gov/pubmed/29905836
http://dx.doi.org/10.1093/nar/gky511
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