By Janet Fang
Posting in Technology
Phylo is an online game that allows players to match up colored blocks corresponding to DNA sequences. Turns out, data from the game are untangling big problems in comparative genomics.
Sometimes, computers just can’t seem to get the answer just right… and that’s where human gamers can make a difference.
Phylo is an online game that allows players to match up colored blocks corresponding to DNA sequences, which have been crowdsourced for this purpose.
And as it turns out, the data gleaned from the game are helping to untangle a major problem in comparative genomics – the study of relationships of genome structure and function across different species. Nature News reports.
A DNA sequence that’s present in many species suggests that it plays an important role in the ultimate function of that particular gene. But it’s very difficult to align roughly similar sequences of DNA in genes that are common to many species. This is called the ‘multiple sequence alignment (MSA) problem.’
To address these problems, Jérôme Waldispühl of McGill University and colleagues decided to create Phylo with our intelligence in mind. “Understanding when something breaks a general rule is very difficult for a computer but that is what human visual intelligence is very good at,” Waldispühl says.
The aim: to improve the sequence alignment of important DNA regions of 521 disease-associated genes from 44 species.
- Sequences are represented by strings of blocks, each with a color corresponding to one of the 4 different bases (the familiar ACGT) that make up DNA.
- By shifting sequences right or left – one block at a time – players try to find the best possible match between sequences for up to 8 different species at a time.
- Players who complete the game within time get to have their alignments in Phylo’s database.
- If their solutions are better than that calculated by MULTIZ – a state-of-the-art alignment program hosted by the University of California, Santa Cruz – their score is displayed in the game's hall of fame.
Since its release in November 2010, the game has attracted over 12,000 users and 350,000 solutions… with gamers beating MULTIZ’s accuracy roughly 70% of the time.
Good to know! With the genomes of 10,000 vertebrate species slated to be sequenced in the next 3–5 years alone, the MSA is only going to get more difficult in future.
The work was published in PLoS ONE last week.
[From Nature News]
Mar 12, 2012