染色质阻断：原核生物结构差异的可扩展全基因组可视化
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes.
作者信息
Sullivan Mitchell John, van Bakel Harm
机构信息
Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America.
出版信息
J Open Source Softw. 2020;5(53). doi: 10.21105/joss.02451. Epub 2020 Sep 23.
Abstract
Chromatiblock is a Python application for visualizing the presence, absence and arrangement of syntenic blocks across large numbers of complete bacterial genomes. Chromatiblock is freely available under a GPL license, for macOS, GNU/Linux and Microsoft Windows from https://github.com/mjsull/chromatiblock/.
摘要
Chromatiblock是一个用Python编写的应用程序，用于可视化大量完整细菌基因组中同线区块的存在、缺失和排列情况。Chromatiblock根据GPL许可免费提供，可从https://github.com/mjsull/chromatiblock/ 下载适用于macOS、GNU/Linux和Microsoft Windows的版本。
相似文献
1
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes.
J Open Source Softw. 2020;5(53). doi: 10.21105/joss.02451. Epub 2020 Sep 23.
2
HapFlow: visualizing haplotypes in sequencing data.
Bioinformatics. 2016 Feb 1;32(3):441-3. doi: 10.1093/bioinformatics/btv551. Epub 2015 Oct 7.
3
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny.
Bioinformatics. 2018 May 1;34(9):1562-1564. doi: 10.1093/bioinformatics/btx757.
4
Automated generation of bacterial resource allocation models.
Metab Eng. 2019 Sep;55:12-22. doi: 10.1016/j.ymben.2019.06.001. Epub 2019 Jun 9.
5
SimPlot++: a Python application for representing sequence similarity and detecting recombination.
Bioinformatics. 2022 May 26;38(11):3118-3120. doi: 10.1093/bioinformatics/btac287.
6
SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.
Bioinformatics. 2018 Sep 1;34(17):3028-3029. doi: 10.1093/bioinformatics/bty212.
7
Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
Bioinform Adv. 2023 Mar 23;3(1):vbad039. doi: 10.1093/bioadv/vbad039. eCollection 2023.
8
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.
Bioinformatics. 2016 Oct 15;32(20):3210-3212. doi: 10.1093/bioinformatics/btw390. Epub 2016 Jun 26.
9
TRANSIT--A Software Tool for Himar1 TnSeq Analysis.
PLoS Comput Biol. 2015 Oct 8;11(10):e1004401. doi: 10.1371/journal.pcbi.1004401. eCollection 2015 Oct.
10
BALLView: an object-oriented molecular visualization and modeling framework.
J Comput Aided Mol Des. 2005 Nov;19(11):791-800. doi: 10.1007/s10822-005-9027-x. Epub 2006 Feb 10.
引用本文的文献
1
Whole-genome probe capture sequencing reveals genomic diversity and characteristics of in Nanjing, China.
Front Microbiol. 2025 May 14;16:1589971. doi: 10.3389/fmicb.2025.1589971. eCollection 2025.
2
Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations.
J Clin Microbiol. 2021 Apr 20;59(5). doi: 10.1128/JCM.03203-20.
3
A Novel Family of Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes.
Front Microbiol. 2020 Dec 2;11:605952. doi: 10.3389/fmicb.2020.605952. eCollection 2020.
本文引用的文献
1
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ.
Nat Commun. 2020 Dec 10;11(1):6327. doi: 10.1038/s41467-020-19777-8.
2
GenomeRing: alignment visualization based on SuperGenome coordinates.
Bioinformatics. 2012 Jun 15;28(12):i7-15. doi: 10.1093/bioinformatics/bts217.
3
Comparing thousands of circular genomes using the CGView Comparison Tool.
BMC Genomics. 2012 May 23;13:202. doi: 10.1186/1471-2164-13-202.
4
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
BMC Genomics. 2011 Aug 8;12:402. doi: 10.1186/1471-2164-12-402.
5
Easyfig: a genome comparison visualizer.
Bioinformatics. 2011 Apr 1;27(7):1009-10. doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28.
6
Mugsy: fast multiple alignment of closely related whole genomes.
Bioinformatics. 2011 Feb 1;27(3):334-42. doi: 10.1093/bioinformatics/btq665. Epub 2010 Dec 9.
7
genoPlotR: comparative gene and genome visualization in R.
Bioinformatics. 2010 Sep 15;26(18):2334-5. doi: 10.1093/bioinformatics/btq413. Epub 2010 Jul 11.
8
Circos: an information aesthetic for comparative genomics.
Genome Res. 2009 Sep;19(9):1639-45. doi: 10.1101/gr.092759.109. Epub 2009 Jun 18.
9
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Genome Res. 2004 Jul;14(7):1394-403. doi: 10.1101/gr.2289704.
Zotero 插件