[Taxacom] Phylogenetic Game

John Grehan jgrehan at sciencebuff.org
Fri Dec 10 11:20:33 CST 2010

This just goes to show that molecular phylogenetics is nothing more than a 'game'. Something I have suspected for a long time.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter Stevens
Sent: Friday, December 10, 2010 12:02 PM
Subject: [Taxacom] Phylogenetic Game

Note that "Players don't need to understand (or even care about)  


Subject: Phylogenetics game

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  
between 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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