Written by: Ethy Cannon1,2, Andrew Wilkey2 and Lacey Sanderson3
1Iowa State University; 2USDA ARS; 3University of Saskatchewan
Integration: Tripal BLAST UI module
The Tripal BLAST UI is a collaborative effort between Legume Federation members to provide a generic, fully featured and customizable interface to the NCBI BLAST suite of tools. CViTjs has been integrated into the Tripal BLAST UI to display location of BLAST hits on the genome. The whole genome view is displayed at the top of the result page, with individual hits displayed below. There is an additional visualization of each hit, as seen below. This provides researchers with a visual indication of how many hits their query received, as well as, the distribution of these hits, which is often very helpful. For example, researchers engaged in association mapping of traits may already have a region of interest in mind and this genome-wide visualization can provide an immediate indication that a given gene is worth further investigation.
Integration: Tripal CViTjs embed
Tripal CViTjs embed was developed by the University of Saskatchewan, Pulse Research Bioinformatics group to provide generic embedding of CViTjs in community web portals built using Tripal. This allows whole-genome wide visualizations to be shared with a greater research community while maintaining the interactive nature of CViTjs. Currently the module makes all diagrams within a CViTjs installation available in one location on the web portal. The diagrams are completely integrated with the portal to provide a consistent user experience and make navigation and exploration of these diagrams intuitive. Future development will make CViTjs diagrams available on Tripal Content pages allowing these web portals to more seamlessly summarize their data in a whole genome context and alleviate the need to manually create each diagram for sharing with the community. The following example shows the distribution of genes on the current Lens culinaris genome assembly (v1.2). Furthermore, the sidebar menu shows the auto-generated “CViTjs Whole Genome Visualization” menu containing the current diagrams available.
CViT is the original Perl application. It produces a static image suitable for publication, as either a PNG or SVG image. Although the functionality of the original CViT is largely available in the more interactive CViTjs, The older CViT does have one advantage over CViTjs: it can render over 100,000 genetic or genomic features, whereas CViTjs is limited to about 2,000. CViT is highly customizable via a configuration file, enabling users to change colors, positions, fonts, and many more aspects of the image. The image below shows gene density on the Arachis duranensis on the left side of each chromosome, and the recombination rates on the right side. This image shows, for example, the effect on recombination rates of an inversion at the end of chromosome 7, and the strange structure of chromosome 8 and its unusual recombination rates. CViT can be downloaded here.
Cannon EKS, Cannon SB. 'Chromosome Visualization Tool: A Whole Genome Viewer'. International Journal of Plant Genomics, Volume 2011, Article ID 373875. http://dx.doi.org/10.1155/2011/373875
Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE and Main D. 'Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic database.' Database, Sept 2013: bat075. https://doi.org/10.1093/database/bat075