The Apple Inc. logo is seen in the lobby of New York City's flagship Apple store
The Apple Inc. logo is seen in the lobby of New York City's flagship Apple store January 18, 2011. REUTERS

Google Inc. (NASDAQ: GOOG) agreed to buy Motorola Mobility Holdings, Inc. (NYSE: MMI) for $40 per share in cash or about $12.5 billion. Jefferies believes Apple Inc. (NASDAQ: AAPL) is likely to strike back in patent war.

"We believe Apple's ability to pressure the Android ecosystem and Android original equipment manufacturer (OEM) device makers has significantly declined following Google's purchase of Motorola Mobility," said Peter Misek, an analyst at Jefferies. "Motorola Mobility in our view had the broadest and deepest patent portfolio amongst the wireless players (about $20 million/essential patent)."

Misek believes Apple's large cash position gives it significant flexibility to respond with its own acquisition. He believes Nokia Corp. (NYSE: NOK), InterDigital Inc. (NASDAQ: IDCC), and Research In Motion Ltd.'s (NASDAQ: RIMM) patents are potential targets.

Of the 17,000 Motorola Mobility patents and 7,000 patents pending acquired by Google, Misek has identified about 500 essential 3G and 4G patents. This implies that each essential patent is worth about $20 million.

Misek believes Google will use Motorola Mobility's patent portfolio as a weapon and not just as a defensive maneuver.

As a countermeasure, Misek expects Apple to closely examine the potential value of the remaining intellectual property portfolios which are Nokia, RIM and InterDigital. He expects Apple to focus on wireless patents that are truly essential and part of the standards.

Misek believes Apple is a licensee of Nokia and pays significant royalties for cross-licensing. He believes Nokia likely has at least 50 essential 4G patents and likely over 100 essential 3G patents.

Misek said Google opted for Motorola Mobility's patent portfolio instead of InterDigital's portfolio, which provides an upper-bound for the value of InterDigital's patents.

But due to the many cross-licensing arrangements and low royalties on some of the patents, it is difficult to gain further clarity on the value of those patents. Apple or another player may be interested but pricing will be key, Misek said.

"By our calculation the BlackBerry maker spent over $5 billion in acquiring and developing its patent portfolio. While RIM has critical security related patents and a unique NOC and Node system, we believe RIM's patent portfolio may be more difficult to value as a stand-alone asset due to its many acquisitions," said Misek.

In the on-going litigation, Misek expects Apple to continue to aggressively pursue its lawsuits with HTC and Samsung in the meantime.

Apple stock moved down 0.76 percent to $380.50 in the pre-market trading on the NASDAQ Stock Market.