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Old 10-28-2013, 09:16 PM   #1
jflowers002
Junior Member
 
Location: Seattle

Join Date: Jan 2013
Posts: 6
Default Trouble with Orthomcl Clusters

I recently did analysis on over 100 genomes within the same phylum using Orthomcl. Sadly, once I finally got the results a couple of weeks later, I discovered that several clusters appeared to have the same function. In fact, in one instance, there were 11 clusters that were likely fructose-2,6-bisphosphatase. I played around with the inflation value a little and found that by it resulted in clusters that appeared to be too mixed in terms of function yet there were still several repeat function clusters. Clearly, this could be a result of bad annotation, but I wanted to see if anyone has had similar problems with Orthomcl cluster prediction.

Thanks!
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