[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
To: TAXACOM
Subject: [Taxacom] Phylogenetic Game
Note that "Players don't need to understand (or even care about)
phylogenetics."
P.
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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