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Video Game Provides Framework For Solving Genomic Sequence Alignment Problems

gene-puzzle-game

Over the past year our genetic understanding of diseases such as Alzheimer’s, diabetes and cancer has been accelerated by thousands of video gamers thanks to an online flash game called Phylo. Phylo is a video game created by Dr. Jérôme Waldispuhl of the McGill Centre for BioInformatics and collaborator Mathieu Blanchette. The game itself is a framework for solving the common problem of multiple sequence alignments in comparative genomics and leverages the visual problem solving skills of online gamers.

The Phylo website explains the background to game:

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.

You can check out Phylo here and the tutorial is definitely recommended. After all, we couldn’t expect you to solve some of the world’s greatest genomic sequencing problems without a little preparation.

Announcement: Video game players advancing genetic research…

Link: Phylo…

*This blog post was originally published at Medgadget*


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