Getting poster data...
Alberto I. Roca, Aaron C. Abajian, David J. Vigerust (University of California, Irvine, USA)A ProfileGrid represents a multiple sequence alignment (MSA) as a matrix color-coded according to the residue frequency occurring at each column position. The JProfileGrid software calculates ProfileGrids of protein families with hundreds of sequences (http://www.biomedcentral.com/1471-2105/9/554). A dynamic interaction with the MSA is achieved by changing the ProfileGrid color scheme, by extracting sequence subsets at selected residues of interest, and by relating alignment information to residue physical properties. Upon analyzing virus protein families such as influenza hemagglutinins with thousands of sequences, it became apparent that the larger datasets were taxing certain design limits of the software. Here we describe new features of the software to accommodate very large MSAs. JProfileGrid now allows sorting and searching the menu list of sequence names. An "overview" mode allows one to visualize the entire ProfileGrid. A new double-pane window feature facilitates dissecting a MSA to detect structural patterns. The ProfileGrid window panes can be independently color-coded and/or used for selecting subsets of sequences.