ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

Background: Multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation. Results: We introduce ProfileGrids that represent a multiple sequence alignment 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 th...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Alberto I. Roca, Albert E. Almada, Aaron C. Abajian
• Keywords: BMCBI 2008, Multiple Sequence Alignment, Sequence Alignment, Stacked Sequence Alignment