ProfileGrids solve the large alignment visualization problem : influenza hemagglutinin example

Introduction The explosion in biological sequence information has led to the generation of large multiple sequence alignments (MSA). For example, the biggest protein family alignment currently in the Pfam database (Wellcome Trust-Sanger Institute) has over 288,000 sequences1. A new generation of alignment programs, such as Clustal Omega2, are available that allow the routine calculation of such large alignments. However, a Nature Methods review3 noted the lack of software tools for visualizing the results of large alignment calculations. Specifically, there was a call for overcoming the conceptual and technical limitations of large data sets to allow one to navigate visually both an overview and the details of an alignment, while having mechanisms to query annotated data. We point out that this conceptual limitation was solved in late 2008 by the introduction of ProfileGrids as a new paradigm for visualizing large multiple sequence alignments4. Here, we report that the remaining technical limitations have been overcome with version 2.0 of the JProfileGrid software, and that therefore, the large alignment visualization problem has now been solved. We use the influenza hemagglutinin protein family as a case study to demonstrate the new features of the software. Abstract Large multiple sequence alignments are a challenge for current visualization programs. ProfileGrids are a solution that reduces alignments to a matrix, color-shaded according to the residue frequency at each column position. ProfileGrids are not limited by the number of sequences and so solves this visualization problem. We demonstrate the new metadata searching and grep filtering features of the JProfileGrid version 2.0 software on an alignment of 11,900 hemagglutinin protein sequences. JProfileGrid is free and available from http://www.ProfileGrid.org.