H-BloX - Calculating the information content or relative entropy from alignment blocks

version 1.47N

online calculation of the information content or the relative entropy within sequence alignment blocks

Do you need help, or want to download H-BloX for local use?
Please read the licence agreement before you use the H-BloX software in your research.

Step 1: Select alphabet of your input block (or type in a custom alphabet)

(There are symbols in the alphabet.)

Step 2: Type in an alignment block (or paste from clipboard)

Step 3: Background distribution of alphabet symbols

(The occurence probability of all valid symbols of the alphabet sums up to %.)

Step 4: Translation of alphabet and alignment block

Select translation table or type in your own translation rules.

Step 5: Check if your input is ok

Used alphabet:
Length of alphabet:
Distribution:

Step 6: Choose output parameters and calculation method (or reset the form)

Color scale
Grey scale
Show sequence block in output table
Fit output table(s) into window

Reference:

Zuegge, J., Ebeling, M., Schneider, G., (2001) H-BloX: visualizing alignment block entropies. J. Mol. Graph. Model., 19 (3-4), 303.

Please cite, when your research makes use of this software.

Further references:

A Mathematical Theory of Communication by Claude E. Shannon This is a very fundamental paper on information theory by Shannon himself.

Information Theory Primer of T. D. Schneider This is a little easier to read and it covers some biological aspects of information theory.

Baldi ,P. and Brunak, S. (1998) Bioinformatics - The Machine Learning Approach. MIT Press, Cambridge, USA.

Durbin, R., Eddy, S., Krogh, A. and Itchinson, G., (1998) Biological Sequence Analysis: Probabilistic models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.

Engelman, D.M., Steitz, T.A. and Golman, A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem., 15, 321.

If you have any questions, comments or ideas about this site, please do not hesitate to contact Jochen Zuegge