gene copy number - how to find how many? (Jun/17/2008 )
As suggested, Southern blotting is the standard method. However, many genes are tandemly duplicated, meaning that two copies lie next to each other. Standard Southern blotting can then give you one signal for two copies. I don't know how reliable quantitative Southern blotting might be. But if you get just one band, does this mean there is only one copy, or are there two (or more) tandem copies?
The correct quantification of gene copies relies on both probe design and restriction enzyme choosen.
The possibility to recognize a tandem repeat depends on how many restriction sites you cut in your sequence and which position they occupy...
also the size of the gene should be known by in silico approach. so you could know what the band is representing. a critical step is during the washes, if the probe binds too weakly you might wash it away and not detect it.