JProfileGrid is a Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. 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.
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BMC Bioinformatics. 2008 Dec 22;9:554. doi: 10.1186/1471-2105-9-554.
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
Roca AI, Almada AE, Abajian AC.