SynVisio: A Multiscale Tool to Explore Genomic Conservation

Abstract

Comparative analysis of genomes is an important area in biological research that can shed light on an organism's internal functions and evolutionary history. It involves comparing two or more genomes to identify similar regions that can indicate shared ancestry and in turn conservation of genetic information. Due to rapid advancements in sequencing systems, high-resolution genome data is readily available for a wide range of species, and comparative analysis of this data can offer crucial evolutionary insights that can be applied in plant breeding and medical research. Visualizing the location, size, and orientation of conserved regions can assist biological researchers in comparative analysis as it is a tedious process that requires extensive manual interpretation and human judgement. However, visualization tools for the analysis of conserved regions have not kept pace with the increasing availability of information and are not designed to support the diverse use cases of researchers. To address this we gathered feedback from experts in the field, and designed improvements for these tools through novel interaction techniques and visual representations. We then developed SynVisio, a web-based tool for exploring conserved regions at multiple resolutions (genome, chromosome, or gene), with several visual representations and interactive features, to meet the diverse needs of genome researchers. SynVisio supports multi-resolution analysis and interactive filtering as researchers move deeper into the genome. It also supports revisitation to specific interface configurations, and enables loosely-coupled collaboration over the genomic data. An evaluation of the system with five researchers from three expert groups coupled with a longitudinal study of web traffic to the system provides evidence about the success of our system's novel features for interactive exploration of conservation.