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Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes
Journal of Heredity ( IF 3.1 ) Pub Date : 2020-07-01 , DOI: 10.1093/jhered/esaa025
Manmohan Pandey 1, 2 , Basdeo Kushwaha 1 , Ravindra Kumar 1 , Prachi Srivastava 2 , Suman Saroj 1 , Mahender Singh 1
Affiliation  

The advent of high throughput next generation sequencing technologies and improved assembly algorithms have ensued in accumulation of voluminous genomic data in public domains. It has opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among the species, facilitating the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization requires computational and bioinformatics skills to prepare input file for the synteny analysis pipeline. The syntenic information in fishes is still in juvenile stage and are scattered in different research domains. Here, we present a web-based tool 'Evol2Circos' to provide a user-friendly GUI- and web-based tool to analyse user specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the circos, bar, dual and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at: 203.190.147.148/evole2circos/.

中文翻译:

Evol2Circos:一种基于网络的工具,用于基因组同线性和共线性分析及其在鱼类中的可视化

高通量下一代测序技术的出现和改进的组装算法随后在公共领域积累了大量基因组数据。它开辟了大规模比较基因组研究的入口,特别是物种间保守同线块的鉴定,促进了基因组组织中保守和变异的进化重要性。Synteny 构建和可视化需要计算和生物信息学技能来为 Synteny 分析管道准备输入文件。鱼类的同线信息尚处于幼年阶段,分散在不同的研究领域。在这里,我们展示了一个基于 Web 的工具“Evol2Circos”,以提供一个用户友好的 GUI 和基于 Web 的工具来分析用户特定数据以进行同线性构建和可视化,并使用圆图、条形图、对偶图和点图方便浏览不同鱼类的同线信息。该工具生成的信息还可用于进一步的下游分析。Evol2Circos 软件工具在 Ubuntu Linux 下测试。网络浏览器、源代码、文档、用户手册、示例数据集和脚本可在线获取:203.190.147.148/evole2circos/。
更新日期:2020-07-01
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