noob: a multiple genome alignment browser

We present a multiple genome alignment browser for sequences from numerous multiple alignments. Our goal is to use information visualization to help users think about how sequences have evolved over time. Our application takes as input a series of multiple alignments in MAF format and outputs an interactive visual display of the data. 1 Information visualization Information visualization has informally been described as “using vision to think” [CMS99]. Information visualization concerns itself with abstract data, whereas scientific visualization concerns itself with physical data measured over space and time (e.g. MRI visualization in medical appliations). Although some of the data we visualize is inherently spatial—sequence fragments along chromosomes, for instance—no attempt is made to display these fragments as they appear in physical reality. Instead, an abstraction is applied to transform the data into a visual format that is informative to the user. This is, in fact, the core problem of information visualization: to find visual abstractions that efficiently convey data attributes to the user. This involves a variety of perceptual considerations which are covered in [War04]and [Kar07]. The aforementioned papers also provide an overview of information visualization as a whole. http://genome.ucsc.edu/FAQ/FAQformat