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BMCBI
2008

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

9 years 1 months ago
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...
Alberto I. Roca, Albert E. Almada, Aaron C. Abajia
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Alberto I. Roca, Albert E. Almada, Aaron C. Abajian
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