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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 screenshots

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
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)

Case Study
A.I. Roca. ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos, BMC Proceedings 8(Suppl 2):S6 (2014)

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.

Last updated: 25-Mar-2015