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:

Step 1 of 5

Click here to submit query.

Step 2 of 5

Right click on the viewer and choose “align sequence” to visualise genome-to-genome co-linearity and divergence.

It is evident from the visualisation that there is a region (from 21.5K to 23K) that is not shared between SARS and Bat SARS.
Step 3 of 5

Go back to viewer in Step 1 and click the button. Choose the region where there is no match as shown opposite and right click, then click on “show query”.

Step 4 of 5

The window opposite will now appear, click on

Step 5 of 5

Leave all parameters at default, but change the target database to: “NCBI Viral RefSeq Genome Release 32” and click on the “Submit query” button.

The region that is highlighted in blue is a potential genic region, but shows no significant homology to any human sequences. It can be hypothesised that this SARS-unique region could be involved in contributing to the easy transmissibility of the SARS virus, in comparison to other coronaviruses.
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