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BioMed Research International
Volume 2016, Article ID 7823429, 7 pages
http://dx.doi.org/10.1155/2016/7823429
Research Article

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

1School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu 211189, China
2The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
3College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
4College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China

Received 6 November 2015; Revised 4 January 2016; Accepted 3 February 2016

Academic Editor: Hesham H. Ali

Copyright © 2016 Yiqing Xu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.