[disclosure: I work for CoSign]
You can use the low or high level APIs to add digital signatures to PDF documents.
For quick and complete integration, check out CoSign's Signature Web Agent .
Update
If you want to control the user interface of the signing process, you can use the CoSign SAPI WebServices API.
Signing using a device against a local certificate: the problem is that storing a digital signature certificate on a PC or server is not recommended because such machines are not Signature Protection Devices (SSCD). Instead, either a centralized, hardened server (such as CoSign), smart cards, or a SAAS solution is considered preferred. And for regulated industries, SSCD is often required.
In addition to security issues, working with local certificates or smart cards / readers / drivers is an expensive administrative burden. A centralized signature server lowers TCO .
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