Wednesday, December 08, 2010

Phylogenetics for Facebook?


a little mad scientist fun for all...

Phylogenetics for Facebook ?
By Allison Proffitt

December 2, 2010 | A pattern-matching puzzle created by bioinformaticians at McGill University lets players sort genetic code. The game, called Phylo, takes advantage of the human brain's efficiency at recognizing and sorting patterns to tackle multiple sequence alignments.

Aligning genetic sequences is traditionally done computationally, but what is a huge computational problem, is a bit easier for the human brain. "There are some calculations that the human brain does more efficiently than any computer can, such as recognizing a face," explained lead researcher Jérôme Waldispuhl of the School of Computer Science in a McGill press release. "Recognizing and sorting the patterns in the human genetic code falls in that category."

Players don't start from scratch, but instead refine data that has already been aligned. "By taking data which has already been aligned by a heuristic algorithm, we allow the user to optimize where the algorithm may have failed," the game creators explain on the site.

All alignments were made available through UCSC Genome Browser and contain sections of human DNA which have been speculated to be linked to various genetic disorders, such as breast cancer. Every alignment is received, analyzed, and stored in a database, where it will eventually be re-introduced back into the global alignment as an optimization. Players can choose which disease they'd like to work on, or be assigned to a random level.

Players don't need to understand (or even care about) phylogenetics though. Rather than strings of As, Ts, Cs, and Gs, players align four colored squares on a grid. Each row of colors represents a sequence from a certain species. Sequences can be moved horizontally and spaced out, but not rearranged or deleted.

 
The goal is to line up columns of colors that represent alignments between the two or more sequences. There will, of course, be gaps in sequences and spots where the two rows don't match. The goal is to find the best tradeoff betwen aligning color and creating gaps. Players try to manually find the best alignment and beat the computer's original alignment score. The first level aligns two sequences, and sequences are added as players advance.

Researchers released the game on Monday after testing. They hope the create a Facebook, iPhone, and Android application versions of the game. Until then, Phylo can be played at
http://phylo.cs.mcgill.ca.

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