Genomic Rearrangement Analysis: Difference between revisions
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==Tutorial:== | |||
Using CoGe to help with Genomic Rearragement Analyses is quite simple: | |||
[[Image:Screen shot 2011-03-11 at 7.58.04 AM.png|frame|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]] | *Pre-configured [[SynMap]] example: http://genomevolution.org/r/2nd9 | ||
# Go to [[SynMap]] | |||
# Select two genomes | |||
# Select the "Analysis Options" tab | |||
# 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) | |||
# Set the "Syntenic Depth" algorithm to [[Quota align]] and have the ratio of syntenic depth set to 1:1 | |||
# Run SynMap | |||
# Use the link "Rearrangement Analysis" located under the "Links and Downloads". This will take you to [http://grimm.ucsd.edu/GRIMM/ GRIMM] for the genomic rearrangement analysis | |||
# 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.]] | |||
==[[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]] | |||
==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]]]] | |||
==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.]] | |||
Latest revision as of 14:08, 11 March 2011
Tutorial:
Using CoGe to help with Genomic Rearragement Analyses is quite simple:
- Pre-configured SynMap example: http://genomevolution.org/r/2nd9
- Go to SynMap
- Select two genomes
- Select the "Analysis Options" tab
- 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)
- Set the "Syntenic Depth" algorithm to Quota align and have the ratio of syntenic depth set to 1:1
- Run SynMap
- Use the link "Rearrangement Analysis" located under the "Links and Downloads". This will take you to GRIMM for the genomic rearrangement analysis
- Run GRIMM
Configuring Quota Align with a 1:1 ratio of syntenic depth to auto-enable the link to GRIMM for genomic rearrangement analysis
SynMap results with link to GRIMM
GRIMM auto-populated by SynMap
GRIMM genomic rearrangement analysis results
