Genomic Rearrangement Analysis

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Using CoGe to help with Genomic Rearragement Analyses is quite simple:

  1. Go to SynMap
  2. Select two genomes
  3. Select the "Analysis Options" tab
  4. Optional: Set the "Merge Syntenic Blocks" algorithm to [[Quota align] and set some number of allowable overlapping genes (10-20 works well for microbes, select 80 for large animal and plant genomes)
  5. Set the "Syntenic Depth" algorithm to Quota align and have the ratio of syntenic depth set to 1:1
  6. Run SynMap
  7. Use the link "Rearrangement Analysis" located under the "Links and Downloads". This will take you to GRIMM for the genomic rearrangement analysis
  8. Run GRIMM

Configuring Quota Align with a 1:1 ratio of syntenic depth to auto-enable the link to GRIMM for genomic rearrangement analysis

Configuring a SynMap analysis to use Quota align with a syntenic depth of 1:1.

SynMap results with link to GRIMM

Syntentic dotplot between two species of Escherichia. X-axis: coli B strain REL606; Y-axis: fergusonii strain ATCC 35469. Syntenic dotplot has boxes drawn around syntenic regions and there is a link to GRIMM for rearrangement analysis. The link to GRIMM will only show if the quota align algorithm has been set and set to a 1:1 ratio. Results may be regenerated at

GRIMM auto-populated by SynMap

Screen-shot from GRIMM server with submission boxes auto-populated when linked to from SynMap

GRIMM genomic rearrangement analysis results

Screen-shot from GRIMM server after performing a rearrangement analysis on two Escherichia genomes.