Introduction Large multiple sequence alignments (MSAs) are taxing current visualization methods such as the traditional stacked sequence depiction. ProfileGrids are a new paradigm for visualizing and analyzing MSAs in a concise representation. For a protein sequence, a ProfileGrid matrix contains positional amino acid counts highlighted according to the frequency of the characters in the alignment. ProfileGrids facilitate comparative nanoanatomy analysis of macromolecules. See the Examples page for a description.
	JProfileGrid software A Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. JProfileGrid provides both command-line support and a graphical user interface. Software has been been tested on the Macintosh, Windows, and Linux platforms and should work on any system supporting the Java Runtime Environment (JRE). JProfileGrid may be obtained from the Downloads page.
	Please cite A.I.Roca, A.E.Almada, and A.C.Abajian, ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family, BMC Bioinformatics 9: 554 (2008)