First import the certificate into the Windows certificate store. See http://tjworld.net/software/codesigning/JKS2PFX.html for this. If you need to use it from an aspnet account, you may want to import it into the machine store (instead of the certificate store of your accounts). Use MMC addin certificates to verify it.
Then use this certificate in your application. In most cases, you will select it by the "DN = ...." property (which you will also see in the MMC).
NTN, Thomas
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