SynaCompare™ is a high-speed comparative genomics application which performs pair-wise comparisons of single and multiple query sequences, chromosomes or whole genomes. The application allows nucleotide-nucleotide, protein-protein, and nucleotide-protein sequence comparisons and presents results in a dynamic “dot-plot” viewer.
Application Example:
Bordetella pertussis is a highly contagious gram-negative bacterium which causes whooping cough in humans. Related species include Bordetella bronchiseptica and Bordetella parapertussis which also infect the respiratory system of other mammals and cause diseases such as kennel cough in dogs and atrophic rhinitis in pigs. Using SynaCompare in the “one to one” nucleotide comparison mode, the genomes of all three bacteria were compared against each other. It was discovered that the B. pertussis genome has a prominent rearrangement (Figure 2 and Figure 3) in comparison to B. bronchiseptica and B. parapertussis which are relatively similar to each other (Figure 4). The significance of this rearrangement to gene regulation in B. pertussis and its relative virulence in humans as compared to other mammals remains unclear. Nonetheless, the result in the SynaCompare dot plot is designed to allow interactive data extraction and further analysis by inference and observation. As shown in Figure 4 users can select a region of interest and right click to conduct further analysis using other SynaSuite applications.
To run the example above, please:
  1. Go to
  2. Click on SynaCompare.
  3. Click on Test Sequence and select the Application Note test sequence by clicking on the “Copy” button next to the sequence. The three test sequences are respective comparisons of B. pertussis, B. bronchiseptica and B. parapertussis.
  4. Set Min.Match Length to 20.
  5. Using the given parameters given, click on Compare to begin your analysis.
Figure 1: SynaCompare input page and parameters.
Figure 2: SynaCompare of Bordetella pertussis Tohoma I to Bordetella parapertussis 12822 shows significant genomic rearrangements.
Figure 3: SynaCompare of Bordetella pertussis Tohoma I to Bordetella bronchiseptica RB50 shows significant genomic rearrangements.
Figure 4: SynaCompare of Bordetella parapertussis 12822 to Bordetella bronchiseptica RB50 shows fewer genomic rearrangements. By selecting a region and right-clicking over the selection, further analysis can be done for the selected area using tools that are provided.

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