SynMap2 和 SynMap3D：基于网络的全基因组同线性浏览器。

SynMap2 and SynMap3D: web-based whole-genome synteny browsers.

机构信息

Genetics GIDP, University of Arizona, Tucson AZ, USA.

Department of Computer Science, University of Arizona, Tucson AZ, USA.

出版信息

Bioinformatics. 2017 Jul 15;33(14):2197-2198. doi: 10.1093/bioinformatics/btx144.

DOI:10.1093/bioinformatics/btx144

PMID:28334338

Abstract

SUMMARY

Current synteny visualization tools either focus on small regions of sequence and do not illustrate genome-wide trends, or are complicated to use and create visualizations that are difficult to interpret. To address this challenge, The Comparative Genomics Platform (CoGe) has developed two web-based tools to visualize synteny across whole genomes. SynMap2 and SynMap3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectively) in responsive, web-based visualization and virtual reality environments. Both tools have access to the extensive CoGe genome database (containing over 30 000 genomes) as well as the option for users to upload their own data. By leveraging modern web technologies there is no installation required, making the tools widely accessible and easy to use.

AVAILABILITY AND IMPLEMENTATION

Both tools are open source (MIT license) and freely available for use online through CoGe ( https://genomevolution.org ). SynMap2 and SynMap3D can be accessed at http://genomevolution.org/coge/SynMap.pl and http://genomevolution.org/coge/SynMap3D.pl , respectively. Source code is available: https://github.com/LyonsLab/coge .

CONTACT

ericlyons@email.arizona.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

目前的基因同线性可视化工具要么专注于小的序列区域，无法说明全基因组的趋势，要么使用复杂，创建的可视化效果难以理解。为了解决这个挑战，比较基因组学平台（CoGe）开发了两个基于网络的工具，用于可视化整个基因组中的基因同线性。SynMap2 和 SynMap3D 允许研究人员在响应式网络可视化和虚拟现实环境中探索全基因组基因同线性模式（分别跨越两个或三个基因组）。这两个工具都可以访问广泛的 CoGe 基因组数据库（包含超过 30000 个基因组），并且用户可以选择上传自己的数据。通过利用现代网络技术，无需安装，使这些工具广泛可访问且易于使用。