Genomic Rearrangement Analysis: Difference between revisions

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


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# Run GRIMM
# Run GRIMM


==Configuring [[Quota Align]] with a 1:1 ratio of syntenic depth to auto-enable the link to GRIMM for genomic rearrangement analysis==
[[Image:Screen shot 2011-03-11 at 7.58.21 AM.png|frame|center|Configuring a [[SynMap]] analysis to use [[Quota align]] with a syntenic depth of 1:1.]]


[[Image:Screen shot 2011-03-11 at 7.58.21 AM.png|frame|left|Configuring a [[SynMap]] analysis to use [[Quota align]] with a syntenic depth of 1:1.]]
==[[SynMap]] results with link to GRIMM==
[[Image:Screen shot 2011-03-11 at 7.58.04 AM.png|frame|center|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 http://genomevolution.org/r/2nd7]]


[[Image:Screen shot 2011-03-11 at 7.58.04 AM.png|frame|left|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 http://genomevolution.org/r/2nd7]]
==GRIMM auto-populated by [[SynMap]]==
[[Image:Screen shot 2011-03-11 at 8.17.49 AM.png|frame|center|Screen-shot from [http://grimm.ucsd.edu/GRIMM/ GRIMM server] with submission boxes auto-populated when linked to from [[SynMap]]]]


[[Image:Screen shot 2011-03-11 at 8.17.49 AM.png|frame|left|Screen-shot from [http://grimm.ucsd.edu/GRIMM/ GRIMM server] with submission boxes auto-populated when linked to from [[SynMap]]]]
==GRIMM genomic rearrangement analysis results==
 
[[Image:Screen shot 2011-03-11 at 8.18.15 AM.png|frame|center|Screen-shot from [http://grimm.ucsd.edu/GRIMM/ GRIMM server] after performing a rearrangement analysis on two Escherichia genomes.]]
[[Image:Screen shot 2011-03-11 at 8.18.15 AM.png|frame|left|Screen-shot from [http://grimm.ucsd.edu/GRIMM/ GRIMM server] after performing a rearrangement analysis on two Escherichia genomes.]]

Latest revision as of 14:08, 11 March 2011

Tutorial:

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 http://genomevolution.org/r/2nd7

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.
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