Possible Clues:

• Convert (information) using a cipher
• Put in cryptic form
• Translate data into a computer program
• Privatize?
• Make unreadable, in a way
• Act as a blueprint for, as DNA for proteins
• Don't let the secret recipe get out for starter of Emerald Fish caught in northeast
• Almost finished penning military leader's cipher
• Make tough to make out
• Make secret garden, almost penetrated by officer