Getting poster data...
Alberto I. Roca (ProfileGrid.org, Irvine, CA, USA)ProfileGrids are a new paradigm for visualization large multiple sequence alignments as a matrix color-coded according to the residue frequency occurring at each column position (http://www.biomedcentral.com/1471-2105/9/554/). The new JProfileGrid v2.0 software was released in 2013 described here: http://f1000research.com/articles/2-2/. We discuss the criteria for paradigms and tools for visualizing large alignments. Procter (2010) suggested that tools should navigate visually both an overview and the details of an alignment while having mechanisms to query annotated data. JProfileGrid accomplishes these tasks in contrast to other methods such as Sequence Logos (& variations like HMM Logos). These do not create interpretable depictions of variable regions or of rare residues. New criteria for "solving" the large alignment visualization challenge now include visualizing specific subgroups of an alignment and correlations between amino acid positions within subgroups. We show that JProfileGrid 2.0 does visualize subgroups using a new metadata feature. Also, complete amino acid correlations are visualized through a novel residue selection feature treating an alignment as a database.