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Software: JProfileGrid for visualizing large multiple sequence alignments
Submitted by Alberto Roca; posted on Friday, January 16, 2009 (1 comment)
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.

AVAILABILITY:
Download at http://www.profilegrid.org/

ARTICLE:
"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)
[link]

REQUESTING COMMENTS:
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, and ProfileGrids.

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Updated JProfileGrid software
Submitted by Alberto Roca; posted on Sunday, June 21, 2009
New JProfileGrid version (v1.2.1) fixes bug that prevented command-line version from working.
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