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The effect of these collections is to filter the results that would have come from the overall Cornell search, allowing only the subset of results that correspond to your list of domains to be reported. The advantage is that with the normal seach dialog you can only specifiy a single domain to filter on - with a collection it can be many domains. Adding a domain to your collection that is outside of the Cornell master list will not cause it to be indexed! You may be wondering what domains are in Cornell's master list.
The org Cornell University Web Knowledgebase has some good information about the Google Search Appliance here...
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