Campbell's CHOWDER SOUP can

Talk on Information Theory in Biology

Thomas Schneider

Logos and walkers: graphical analysis of splice junctions and other binding sites, with clinical application

Movie of a walker

sequence walker

abstract:

A graphical method is presented for displaying how binding proteins and other macromolecules interact with individual bases of nucleotide sequences. Characters representing the sequence are either oriented normally and placed above a line indicating favorable contact, or upside-down and placed below the line indicating unfavorable contact. The positive or negative height of each letter shows the contribution of that base to the average sequence conservation of the binding site, as represented by a sequence logo. These sequence `walkers' can be stepped along raw sequence data to visually search for binding sites. Many walkers, for the same or different proteins, can be simultaneously placed next to a sequence to create a quantitative map of a complex genetic region. One can alter the sequence to quantitatively engineer binding sites. Database anomalies can be visualized by placing a walker at the recorded positions of a binding molecule and by comparing this to locations found by scanning the nearby sequences. The sequence can also be altered to predict whether a change is a polymorphism or a mutation for the recognizer being modeled.

Johns Hopkins Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
Wednesday, October 1, 1997 at 1:30PM

Note: This is the same talk as http://schneider.ncifcrf.gov/bitcs/schneider1997sep30.html and http://schneider.ncifcrf.gov/bitcs/schneider1997oct14.html

Host: Cynthia Wolberger
Seminar arrangements:
Kathleen Kolish (kathleen_kolish@qmail.bs.jhu.edu)
410-955-8712 or FAX 410-550-6910

This announcement is at http://schneider.ncifcrf.gov/bitcs/schneider1997oct1.html

Cover of Nucleic Acids Research November 1997 showing
sequence logos for human donor and acceptor splice junction
sites above 5 example sequence walkers for each splice
junction.
Sequence logos and walkers. At the top of the figure sequence logos for human donor and acceptor sites depict the DNA sequence conservation by stacks of letters. Within each stack the height of each letter is proportional to the base frequency at that position in the binding site. Below the sequence logos, five examples of individual binding sites are shown as walkers. The height of each letter shows its contribution to the average sequence conservation in the sequence logo on the top. (This figure will be the cover of Nucleic Acids Research volume 25, issue 21.)

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Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers
Schneider Lab
.
origin: 1997 September 15
updated: 2006 Jan 26 color bar
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