H-BloX: visualizing alignment block entropies.

Abstract H-BloX is a web-based JavaScript application that allows the calculation and visualization of Shannon information content or relative entropy (Kullback-Leibler ‘distance’) within sequence alignment blocks. The application was designed for use in both teaching and research. Amino acid, nucleic acid sequences, or any other type of aligned chemical structures may serve as the input. Various interpretations of the meaning of ‘entropy’ or ‘information content’ are possible, including treatment as a chemical diversity measure or the degree of feature conservation. For analysis of numerical data by H-BloX, values must be converted to a user-defined character alphabet before computation of entropy or information content. H-BloX was successfully applied to feature identification in Escherichia coli signal peptides and their cleavage sites. Characteristic known features became visible, e. g., the hydrophobic core region and the well-known ‘−3,−1’ cleavage site pattern. Based on the H-BloX analysis, the hydrophobic core is centered at amino acid residue position 13, counting from the N-terminal end of the protein precursor sequence. This result was obtained by using a built-in feature of H-BloX that enables conversion of amino acid sequences to a different alphabet that is based on hydrophobicity assigments. H-BloX can be accessed online or downloaded as HTML/JavaScript at http://bopwww.biologie.uni-freiburg.de/∼bioinfo/HBloX/html/index.html