Viral genomic diversity analysis and phylogenetics are critical for understanding host-pathogen interactions, disease progression and vaccine design. However, current approaches for whole-genome comparative genomics are either too slow, require custom databases to be built, or generate results which are not suitable for easily accessible downstream whole genome analysis.
SynaCompare is a free online, high-speed comparative genomics application that executes pair-wise comparisons of whole genomes against single or multiple target genomes. The output is displayed in a dot plot viewer that enables downstream functional annotation and analysis of genome conservation and co-linearity.
In this example, a whole genome analysis of the SARS virus was carried out. Previous studies have indicated that bats are natural reservoirs of SARS-like coronaviruses, hence the SARS virus was compared to the Bat SARS CoV Rp3, as well as to all viruses in the NCBI RefSeq Viral Genome database (release 32).
To begin analysis, please follow the steps below: