One of the clunkier aspects of the mobile experience is the lack of a seamless transition from app to app.

For instance, when LinkedIn sends you an email about a new connection, the accompanying link sends you to LinkedIn’s homepage rather than its app. If you’re a retailer advertising on mobile, those who click through will either go to your homepage or to the front door of your app, rather than to a page where they can buy a product.

A few startups are looking to change that, including URX, Quixey and Cellogic’s All three come at it differently, but their pitch is based around improving the mobile ad experience.

URX officially launched earlier this month with $3 million in funding from a large group including Jamie Lee Curtis, Google Ventures and TechCrunch founder Michael Arrington. The company aims to enable advertising that sends a user from, say, a mobile banner ad to precisely the right page within an app. For instance, if you have the LivingSocial app installed and you have a penchant for deals for home improvement products, then the company (an actual URX partner) can serve up a targeted ad that send them directly to that deal.

Quixey, meanwhile, aims to be a search engine for the mobile era. Liron Shapira, the CTO and founder of Quixey, foresees a day in which searching your phone for “Chipotle” might call up the app or the Yelp page that will direct you to the nearest location. This month, the company raised $50 million in series C funding led by China’s Alibaba Group.

Isreal’s Cellogic earlier this year launched, a deep link service. Itamar Weisbrod, the company’s founder, says his future goal is to further native advertising on mobile, though he’s now focused on helping developers make it more accessible and linkable.

In August, Cellogic launched a mobile ad retargeting network. “Generally, I’d say that native advertising is just one of many use cases for native deep links,” he says. “So as of now, we’re powering more retargeting ads, some look like the usual banners, but some are actually native ads as well.”

Since the idea is to have an HTTP link that would allow for seamless navigation through mobile apps, a good analogy in the desktop world is Bitly. Bitly, which launched in 2008 with a URL shortening technology, was at the forefront of the social web. The company has cooled off of late as Twitter has released its own URL shortener, but serves as a template for startups that see a similar opportunity with mobile.

As with Bitly, though, there may never be a proprietary deep linking standard. Since deep linking will often be invisible to users, there’s less of a branding opportunity. That’s why the companies are using deep links to promote other businesses.

Now that Facebook has put its heft behind deep links, the technology has a good opportunity to spread quickly.

For mobile advertisers, the big change will be a move away from the walled garden approach to apps. As Shapira says, “apps really are just part of the web.”

For marketers, that means that unless a consumer has downloaded your app, they won’t see your ad. Hence there will be be more pressure to get consumers to download your apps. As a 2011 Localytics study showed, that’s not so easy — some 26% of consumers download an app and never use it again. However, another 26% report using an app more than 10 times. Translation: It’s tough to get people to use your app, but there’s a lot of potential upside.

At least that’s if deep links take off as expected. Not everyone thinks so. Chris Cunningham, co-founder and CEO of mobile ad firm Appssavvy, says he thinks the technology — which has been around for years — is being overhyped. “I’m not entirely sure that this opens up a huge avenue for developers beyond some commerce sites,” he says. “It doesn’t feel like a seismic, groundbreaking change.”

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