Computing and visually analyzing mutual information in molecular co-evolution

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 that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for 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 normalization...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Sebastian Bremm, Tobias Schreck, Patrick Boba, Stephanie Held, Kay Hamacher
• Keywords: BMCBI 2010, Mutual Information, Mutual Information Matrix, Proper Normalizations