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Will google strip the .com and still rank me well for the search term "Big Blue Widgets" or only for "Big Blue Widgets.com"?
This would make sense so Google knows pepsi.com is still Pepsi, for example, but I just wanted to check before I commit to it.
I assume the anchor text is just big blue widgets.com and then descriptive text.
In your example (with spaces), Google will index you for "big", "blue" and "widgets.com".
If the link is "big-blue-widgets.com" it will be the same as above. Hence keyword domain advantage.
If the link is "bigbluewidget.com" then you get no keyword anchortext.
It makes sense to ignore the domain if google wants to tackle keyword domain advantage, but at present I don't think they do.
The words surrounding anchor text, perhaps up to five, are related to the link, so "custom" will be associated with the link text. In this respect a better link would be "Big(space)blue(space)widgets(space).com - Custom made widgets.
Soapystar is correct. The period is seen as a word break.
Although correct this is not really the issue (I think) or question you need an anwer for.
Link anchors are the concern as MHes has pointed out.
If as a link anchor both of these example would depreciate the weighing value of the anchor for a search query on blue widget
A link anchor such as blue widget [bluewidgets.com].com (where the dot.com is not part of the link anchor) or; BlueWidget.com is a reseller of blue widgets [bluewidgets.com]. -- would add more weight from off-part relevancies.