ArticleNucleic acids research2018
KnotGenome: a server to analyze entanglements of chromosomes.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.Nucleic acids research · 2024Article
- Topoly: Python package to analyze topology of polymers.Briefings in bioinformatics · 2021Article
- Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo.The EMBO journal · 2021Article
- GLN: a method to reveal unique properties of lasso type topology in proteins.Scientific reports · 2020Article
- Chromatin Is Frequently Unknotted at the Megabase Scale.Biophysical journal · 2020Article
- Knot_pull-python package for biopolymer smoothing and knot detection.Bioinformatics (Oxford, England) · 2020Article
- Article
- Defining and detecting links in chromosomes.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
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