Gamers outdo computers at matching up disease genes – reports Stephen Strauss in a news article published on March 12th for the journal Nature.
The hope that swarms of gamers can help to solve difficult biological problems has been given another boost by a report in the journal PLoS One1, showing that data gleaned from the online game Phylo are helping to untangle a major problem in comparative genomics.
The game was created to address the ‘multiple sequence alignment (MSA) problem’, which refers to the difficulty of aligning roughly similiar sequences of DNA in genes common to many species. A DNA sequence that is conserved across species suggests that it plays an important role in the ultimate function of that particular gene.
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A Closer Look at Phylo: Phylo is a challenging flash game in which every puzzle completed contributes to mapping diseases within human DNA.
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. This is due in part to the sheer size of the genome, which consists of roughly three billion base pairs, and the increasing computational complexity resulting from each additional sequence in an alignment.
By abstracting multiple sequence alignment to manipulating patterns consisting of coloured shapes, the creators of Phylo have adapted the problem to benefit from human capabilities to solve visual problems and recognise patterns. Taking data which has already been aligned by a heuristic algorithm, Phylo allows the user to optimize where the algorithm may have failed.
All alignments contain sections of human DNA which have been speculated to be linked to various genetic disorders, such as breast cancer made available through UCSC Genome Browser. 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.
Watch Phylo’s Video Tutorial
Source: Nature News, Phylo.
