Computing and Visually Analyzing Mutual Information in Molecular Co-Evolution

Sebastian Bremm, Tobias Schreck, Patrick Boba , Stephanie Held and Kay Hamacher

Abstract

Background: Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information - after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.
Results:To visually analyze mutual information we

developed a matrix visualization tool. It allows to take different views on the mutual information matrix by ltering, sorting, weighting, and zooming functionality. Thereby, the user can interactively navigate a huge matrix in real-time and search for e.g., patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to Z scores with respect to the null model.
Conclusions: The new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users applying in real-world
research. The software can also be used for visual analytics of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in Java and free for academicusage under a GPL license.


Installation Information

For running the programs, a installation of Java (>= Version 1.5) is needed. Unpack the archive after downloading it. There are two folders contained.
Micato takes the part of calculating the mutual information. Starting it with the "startMicato.bat" file produces a demo-output. For further information please see the related readme file.
Contact for technical questions:
Patrick Boba: icon email boba@bio.tu-
MatrixVis visualizes the previously calculated mutual information. Starting it without parameters or the "startMatrixVis.bat" leads to a visualization of the demo data contained in the data folder. For further information please see the related readme file.
Contact for technical questions:
Sebastian Bremm: icon email sebastian.bremm@gris.tu-
If more informations are needed, feel free to contact one of the authors.

Downloads

This software is developed by the Computational Biology and Interactive-Graphics Systems groups at Technische Universität Darmstadt. It is provided for free use under the GNU License for Academic Use.
Download micatoMatrixVis.zip

 

Kontakt

Technische Universit├Ąt Darmstadt

Graphisch-Interaktive Systeme

Fraunhoferstr. 5
64283 Darmstadt

Tel. +49 6151 155 679

icon email office@gris.tu-



Technische Universit├Ąt Darmstadt

AG Bioinformatics and theo. Biology

Schnittspahnstr. 10
64287 Darmstadt

Tel. +49 6151 16-5318

icon email hamacher@bio.tu-

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