Description: SynaCompare is an application that performs high-speed, multi-genome comparative genomics analysis of viral, bacterial or even whole mammalian genomes.

Application Example: Using the Human Herpesvirus 1 genome sequence to cross-check for inverted regions across species

A fragment of the Human Herpesvirus 1 (NC_001806.1) from position 128,104 to 151,676 (23573bp) was queried against Human Herpesvirus 2 (NC_001798.1).

Using the default parameters, SynaCompare clearly shows a region of inversion between the alignments. This inverted region is conserved in most of the Herpesvirus family.

To try SynaCompare, please:

1. Click here and then click on the “Access Now” button
2. Click on SynaCompare and make sure the query type is set to Nucleotide-nucleotide.
3. Click on the ‘test sequence’ button and get the herpesvirus 1 sequence fragment into the ‘Sequence’ box by clicking on the ‘Copy’ button.
4. The ‘Viral genomes’ should already be pre-selected with human herpesvirus 2 in the target expression box.
5. Using the default parameters, click on ‘COMPARE’ to begin your analysis.
6. Once you have your results in a dot plot graph, you can manipulate the graph to zoom into a particular area of interest as well as perform any other type of analysis such as mining for functional and structural annotations with the buttons on the right.

Note: Query size limit for free unregistered users for SynaCompare is set to 25Kbp.