Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
Nucleic Acids Res. 2018 Jul 2;46(W1):W17-W24. doi: 10.1093/nar/gky511.
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/.
KnotGenome 服务器使用染色体的三维坐标文件作为输入，实现了对染色体模型数据的拓扑分析。它特别能够检测单条染色体中的原始和复合结，以及染色体之间的连接。染色体的扭结复杂性以矩阵图的形式呈现，揭示了整个多核苷酸链及其每个亚链的结类型。连接通过高斯连接积分和 HOMFLY-PT 多项式来确定。纠缠的染色体以直观的方式以图形方式呈现。在分析之前，也可以通过短时间的分子动力学松弛结构。KnotGenome 可在 http://knotgenom.cent.uw.edu.pl/ 免费获取。
