Genomic Rearrangement Analysis: Difference between revisions

Revision as of 14:04, 11 March 2011

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

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

@@ Line 1: / Line 1: @@
+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 [http://grimm.ucsd.edu/GRIMM/ GRIMM] for the genomic rearrangement analysis
+# Run GRIMM
 [[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.]]