Rs,Rf_Evolution_of_Binding_Sites individual slides

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This talk/slide show explains these papers:
- Information content of binding sites on nucleotide sequences JMB 188: 415, 1986.
- Evolution of Biological Information NAR 28: 2794, 2000
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The data are from:
- T. D. Schneider et al J. Mol. Biol., 188, 415-431, 1986
- R. M. Stephens and T. D. Schneider J. Mol. Biol., 228, 1124-1136 1992
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Evolution of Binding Sites: The Movie
(window, web link)
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Sequence logo of the final evolved binding sites.
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You never know how it might turn out!

The image was derived from: http://www.dinosauria.com/gallery/chris/chris.html, copyright 1998 Christopher Srnka (theclaw10@home.com).
20 $Shannon Information Measure of Binding Site Patterns Information is measured as a decrease in uncertainty: $R = H_{before} - H_{after}$ (bits per symbol). Before binding there are 4 possible bases at each position $l$, so the uncertainty is: $H_{before}(l) = \log_2 4$ (bits per base) \approx 2 . After binding the uncertainty depends on the frequencies of bases $b$ at positions $l$ in a binding site, $f(b,l)$: $H_{after}(l) = -\sum b \in \{A,C,G,T\}$ $f(b,l) \log_2 f(b,l)$ (bits per base). The information at a position $l$} is: $\rsequence(l) & = & H_{before}(l) - H_{after}(l) & \approx & 2 - H_{after}(l)$ (bits \emph{per base}). The total site information is: $\rsequence & = & \sum_l \left( H_{before}(l) - H_{after}(l)\right) & \approx & 2l - H_{after}$ (bits \emph{per site}). As $H_{after} \downarrow$, $\rsequence \uparrow$$
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The image was derived from: http://www.ndirect.co.uk/~luisrey/, copyright Luis Rey (luisrey@ndirect.co.uk ). It is described at http://www.ndirect.co.uk/~luisrey/html/bary256.htm.

2011Aug17.20:35:55