Software: JProfileGrid for visualizing large multiple sequence alignments Print
Written by Sebastian Bassi   
Monday, 16 March 2009 18:48
Comparative nanoanatomy and phylogenetic studies of macromolecules depend upon multiple sequence alignments (MSAs). However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.

We introduce ProfileGrids that represent a MSA as a matrix color-coded according to the residue frequency occurring at each column position. JProfileGrid is a Java application for computing and analyzing ProfileGrids. A dynamic interaction with the alignment information 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. Conserved family motifs can be identified by the overlay of similarity plot calculations on a ProfileGrid. Figures suitable for publication can be generated from the saved spreadsheet output of the colored matrices as well as by the export of conservation information for use in the PyMOL molecular visualization program.

"ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family"
Alberto I Roca*, Albert E Almada, Aaron C Abajian
BMC Bioinformatics 9:554 (2008)

Any feedback on the ProfileGrid paradigm and the Java software are appreciated. We are especially interested in any citations to novel alignment representation paradigms that were _not_ mentioned in the background section of our paper. Specifically, are there any other alignment visualization paradigms besides the following: the traditional stacked sequence lists; boxing, coloring, & shading of stacked sequences; regular expressions; major components; sequence logos; graphical "overviews" (such as by Jalview or CINEMA); similarity value plots; partial order graphs; dot plots; and ProfileGrids.