Video game players advancing genetic research

A sequence alignment is a way of arranging the sequences of D.N.A, R.N.A or protein to identify regions of similarity. These similarities may be consequences of functional, structural, or evolutionary relationships between the sequences. From such an alignment, biologists may infer shared evolutionary origins, identify functionally important sites, and illustrate mutation events. More importantly, biologists can trace the source of certain genetic diseases.

Traditionally, multiple sequence alignment algorithms use computationally complex heuristics to align the sequences. Unfortunately, the use of heuristics do not guarantee global optimization as it would be prohibitively computationally expensive to achieve an optimal alignment…

…Humans have evolved to recognize patterns and solve visual problems efficiently. By abstracting multiple sequence alignment to manipulating patterns consisting of coloured shapes, we have adapted the problem to benefit from human capabilities. By taking data which has already been aligned by a heuristic algorithm, we allow the user to optimize where the algorithm may have failed.

Last week the researchers released the results computed from the Phylo solutions collected over the last year, together with an improved version of Phylo for mobile devices. The game currently has over 17,000 registered users and since it was launched in November of last year, the researchers have received more than 350,000 solutions to sequence alignment problems.

Thousands of video game players have helped significantly advance our understanding of the genetic basis of diseases such as Alzheimer’s, diabetes and cancer over the past year. They are the users of a web-based video game developed by Dr. Jérôme Waldispuhl of the McGill School of Computer Science and collaborator Mathieu Blanchette. Phylo is designed to allow casual game players to contribute to scientific research by arranging multiple sequences of coloured blocks that represent human DNA. By looking at the similarities and differences between these DNA sequences, scientists are able to gain new insight into a variety of genetically-based diseases.

The researchers are releasing the results computed from the solutions collected over the last year today, together with an improved version of Phylo for tablets.

Over the past year, Phylo’s 17,000 registered users have been able to simply play the game for fun or choose to help decode a particular genetic disease. “A lot of people said they enjoyed playing a game which could help to trace the origin of a specific disease like epilepsy,” said Waldispuhl. “There’s a lot of excitement in the idea of playing a game and contributing to science at the same time,” Blanchette agreed. ”It’s guilt-free playing; now you can tell yourself it’s not just wasted time.”

Waldispuhl and his students came up with the idea of using a video game to solve the problem of DNA multiple sequence alignment because it is a task that is difficult for computers to do well. “There are some calculations that the human brain does more efficiently than any computer can. Recognizing and sorting visual patterns fall in that category,” explained Waldispuhl. “Computers are best at handling large amounts of messy data, but where we require high accuracy, we need humans. In this case, the genomes we’re analyzing have already been pre-aligned by computers, but there are parts of it that are misaligned. Our goal is to identify these parts and transform the task of aligning them into a puzzle people will want to sort out.”

So far, it has been working very well. Since the game was launched in November 2010, the researchers have received more than 350,000 solutions to alignment sequence problems. “Phylo has contributed to improving our understanding of the regulation of 521 genes involved in a variety of diseases. It also confirms that difficult computational problems can be embedded in a casual game that can easily be played by people without any scientific training,” Waldispuhl said. “What we’re doing here is different from classical citizen science approaches. We aren’t substituting humans for computers or asking them to compete with the machines. They are working together. It’s a synergy of humans and machines that helps to solve one of the most fundamental biological problems.”

Source:http://medgadget.com/2011/12/online-video-game-helps-to-solve-genetic-origins-of-diseases.html,http://www.mcgill.ca/newsroom/news/item/?item_id=212750

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