I was extracting fosmid DNA from the ecoli clone and extracted the fosmid using is the Plasmid DNA Miniprep Kit. However, the extract fosmids are less in quantity and not qualified for sequencing. Thus, is the Plasmid DNA Miniprep Kit work well for extracting fosmid DNAs? or any other alternative?
The F plasmid origin in a Fosmid is going to replicate at a much smaller copy number than most plasmids you've probably worked with, there's only going to be 1-2 per E. coli cell. For comparison the "low copy" p15a origin that's pretty common in labs has a copy number of around 10-20. It's normal to get very low yield from a miniprep of these plasmids, even without an insert. If you have a large insert the yields will be even lower.
Some people do maxipreps of these and concentrate them after elution to make up for it, especially if they need them at concentrations for sequencing.
Some BACs/Fosmids contain a 2nd, higher copy origin which is inducible to avoid that.
You can always start with more cells (since your vector is low copy) and just use an alkaline lysis plus subsequent spermidine precipitation: Article Purification of plasmid DNA using selective precipitation by...
This takes longer than the kit, but pDNA is of great quality for most purposes and the yield is higher than from kits (most of the pDNA is the neutralization buffer will be captured; though, this is most critical for high copy plasmids whose amounts simply far exceed the binding capacity of mini-prep columns).
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