Sequence walkers: a graphical method to
display how binding proteins interact with DNA or RNA
sequences
Thomas D. Schneider
National Cancer Institute, Frederick Cancer Research and Development Center, Laboratory of Mathematical Biology, PO Box B, Frederick , MD 21702-1201,USA
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.
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4408-4415 6095 words, 6 figures, 1 tables, 46 references, 51745 bytes.
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See also the companion paper: Information Content of Individual Genetic Sequences
For more infomation see: Individual Information Theory and Sequence Walkers
US patent 5867402Material in this paper is covered by US patent 5867402. Programs using these methods may not be redistributed or used without a signed agreement with the National Institutes of Health. Please contact us at: http://www.lecb.ncifcrf.gov/~toms/contacts.html |
In Figure 2, replace the "&" in the figure legend with "^".
Schneider Lab.
origin: 1997 November 24
updated: 2005 May 30