cosmid clone sequencing (novel genes)

[mjkang]

Hello, all
I am planning to use Solexa sequencing facility with my bacterial cosmid clones. I don't have many background information about this sequence facility however, it looks like reference sequence is very critical.
The problem of my gene is that I did not exact reference sequences instead, I do have similar gene clusters sequence information.

Dose anyone can get me some ideas or comments about my sequencing?
And there are two strains (same genus) whole genomes were sequenced.

Thanks in advance.