Visualizing genome synteny with xmatchview

In genomics research, the visual representation of DNA sequences is of prime importance. When displayed with additional information, or tracks, showing the position of annotated genes, alignments of sequence of interest, etc., these displays facilitate our understanding of genome and gene structure, and become powerful tools to assess the relationship between various sequence data. They can be used for troubleshooting sequence assemblies, in-depth sequence analysis, and eventually find their way in publications and oral presentations as they often translate complex and abundant data succinctly, with esthetically pleasing images. Here, I introduce xmatchview and xmatchview-conifer, two python applications for comparing genomes visually and assessing their synteny. Availability: https://github.com/warrenlr/xmatchview

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

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.