VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
Yiqing Xu1, Changwei Bi2, Guoxin Wu3
1School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu 211189, China; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu 210037, China; College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
Background:
In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many analysis software packages are not effective in visualizing results. Problems include lack of graphic visualization, simple representation, or inextensible format of outputs. Moreover, higher throughput sequencing technology requires higher resolution image output.
Implementation:
To fill this gap, this paper publishes VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).
Result:
Users can upload sequence alignments from blast and collinearity relationship from the synteny analysis tools. The website can generate the vector or raster graphical results automatically. We also provide a java-based bytecode binary to enable the command-line execution.
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