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.
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
Java Runtime Environment (JRE).
JProfileGrid may be obtained from the Downloads page.
version 2.0 software: A.I.Roca, A.C.Abajian, D.J. Vigerust. ProfileGrids solve the large alignment visualization problem: influenza hemeagglutinin example. F1000Research 2: 2 (2013)
version 1.0 software: 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)
Bioinformatics leader mentions ProfileGrids Des Higgins: Visualizing multiple sequence alignments from VIZBI 2011.
Des Higgins gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments.