David Cox of North Carolina State University has created a new visualization method for DNA sequences that he’s calling “symbolic scatter plots”.
His technique starts out similar to Blast, he says, in that it takes the sequence at hand and breaks it up into small words. Whereas Blast computationally plugs those words into a database to find similar matches, his method simply maps the words. In his case those words are 3-mers that correspond to one of 64 possible choices because there are 64 possible combinations of three nucleotides. Each 3-mer is represented as a point on the scatter plot, zero through 63, with that number serving as the y-coordinate. The x-axis is the order that the 3-mer appears in the genetic sequence. Cox designed the symbolic scatter plot so that those 3-mers that correspond to the same amino acid are adjacent to each another.
It’s a good use of “human in the middle” visualization where he’s attempting to replace completely automated systems with tools to make use of the superior human vision system to better discover patterns. His work will be presented at the 2009 International Conference on Bioinformatics and Computational Biology in Las Vegas.
